NCBI has a useful tool that collect the information of all transcripts ID versions and allows you to see differences. Here one example

https://www.ncbi.nlm.nih.gov/nuccore/NM_002734?report=girevhist

I am interested to see if there are differences in the sequence between transcript versions. The website provides a BLAST analysis such as the one I provided below.

In the sequence comparison, I can see that sometimes the base in the subject is capital while in the opposite is lowercase. This is not considered a mismatch by BLAST.

My question is what does this mean???

I show an example here

 Query  61    AGCTCGGTAcgccgccgcctcgcacccgcagcctcgcgcccgccgccgcccgTCCCCAGA  120
              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
 Sbjct  112   AGCTCGGTACGCCGCCGCCTCGCACCCGCAGCCTCGCGCCCGCCGCCGCCCGTCCCCAGA  171

and the almost complete BLAST result here:

 Accession  Gi  Update Date
NM_002734.5 1779521771  Mar 21, 2024 08:35 PM
NM_002734.4 443497962   Sep 25, 2019 01:48 AM
BLASTN 2.15.0+


Reference: Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb
Miller (2000), "A greedy algorithm for aligning DNA sequences", J
Comput Biol 2000; 7(1-2):203-14.



Database: User specified sequence set (Input: /dev/shm/girevhist_2QCl0WI).
           1 sequences; 4,325 total letters



Query= NM_002734.5 Homo sapiens protein kinase cAMP-dependent type I
regulatory subunit alpha (PRKAR1A), transcript variant 1, mRNA

Length=4253
                                                                      Score     E
Sequences producing significant alignments:                          (Bits)  Value

NM_002734.4 Homo sapiens protein kinase cAMP-dependent type I reg...  7854    0.0  


>NM_002734.4 Homo sapiens protein kinase cAMP-dependent type I regulatory 
subunit alpha (PRKAR1A), transcript variant 1, mRNA
Length=4325

 Score = 7854 bits (4253),  Expect = 0.0
 Identities = 4253/4253 (100%), Gaps = 0/4253 (0%)
 Strand=Plus/Plus

Query  1     GGAGCTGTCGCCTAGCCGCTATCGCAGAGTGGAGCGGGGCTGGGAGCAAAGCGCTGAGGG  60
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  52    GGAGCTGTCGCCTAGCCGCTATCGCAGAGTGGAGCGGGGCTGGGAGCAAAGCGCTGAGGG  111

Query  61    AGCTCGGTAcgccgccgcctcgcacccgcagcctcgcgcccgccgccgcccgTCCCCAGA  120
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  112   AGCTCGGTACGCCGCCGCCTCGCACCCGCAGCCTCGCGCCCGCCGCCGCCCGTCCCCAGA  171

Query  121   GAACCATGGAGTCTGGCAGTACCGCCGCCAGTGAGGAGGCACGCAGCCTTCGAGAATGTG  180
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  172   GAACCATGGAGTCTGGCAGTACCGCCGCCAGTGAGGAGGCACGCAGCCTTCGAGAATGTG  231

Query  181   AGCTCTACGTCCAGAAGCATAACATTCAAGCGCTGCTCAAAGATTCTATTGTGCAGTTGT  240
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  232   AGCTCTACGTCCAGAAGCATAACATTCAAGCGCTGCTCAAAGATTCTATTGTGCAGTTGT  291

Query  241   GCACTGCTCGACCTGAGAGACCCATGGCATTCCTCAGGGAATACTTTGAGAGGTTGGAGA  300
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  292   GCACTGCTCGACCTGAGAGACCCATGGCATTCCTCAGGGAATACTTTGAGAGGTTGGAGA  351

Query  301   AGGAGGAGGCAAAACAGATTCAGAATCTGCAGAAAGCAGGCACTCGTACAGACTCAAGGG  360
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  352   AGGAGGAGGCAAAACAGATTCAGAATCTGCAGAAAGCAGGCACTCGTACAGACTCAAGGG  411

Query  361   AGGATGAGATTTCTCCTCCTCCACCCAACCCAGTGGTTAAAGGTAGGAGGCGACGAGGTG  420
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  412   AGGATGAGATTTCTCCTCCTCCACCCAACCCAGTGGTTAAAGGTAGGAGGCGACGAGGTG  471

Query  421   CTATCAGCGCTGAGGTCTACACGGAGGAAGATGCGGCATCCTATGTTAGAAAGGTTATAC  480
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  472   CTATCAGCGCTGAGGTCTACACGGAGGAAGATGCGGCATCCTATGTTAGAAAGGTTATAC  531

Query  481   CAAAAGATTACAAGACAATGGCCGCTTTAGCCAAAGCCATTGAAAAGAATGTGCTGTTTT  540
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  532   CAAAAGATTACAAGACAATGGCCGCTTTAGCCAAAGCCATTGAAAAGAATGTGCTGTTTT  591

Query  541   CACATCTTGATGATAATGAGAGAAGTGATATTTTTGATGCCATGTTTTCGGTCTCCTTTA  600
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  592   CACATCTTGATGATAATGAGAGAAGTGATATTTTTGATGCCATGTTTTCGGTCTCCTTTA  651

Query  601   TCGCAGGAGAGACTGTGATTCAGCAAGGTGATGAAGGGGATAACTTCTATGTGATTGATC  660
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  652   TCGCAGGAGAGACTGTGATTCAGCAAGGTGATGAAGGGGATAACTTCTATGTGATTGATC  711

Query  661   AAGGAGAGACGGATGTCTATGTTAACAATGAATGGGCAACCAGTGTTGGGGAAGGAGGGA  720
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  712   AAGGAGAGACGGATGTCTATGTTAACAATGAATGGGCAACCAGTGTTGGGGAAGGAGGGA  771

Query  721   GCTTTGGAGAACTTGCTTTGATTTATGGAACACCGAGAGCAGCCACTGTCAAAGCAAAGA  780
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  772   GCTTTGGAGAACTTGCTTTGATTTATGGAACACCGAGAGCAGCCACTGTCAAAGCAAAGA  831

Query  781   CAAATGTGAAATTGTGGGGCATCGACCGAGACAGCTATAGAAGAATCCTCATGGGAAGCA  840
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  832   CAAATGTGAAATTGTGGGGCATCGACCGAGACAGCTATAGAAGAATCCTCATGGGAAGCA  891

Query  841   CACTGAGAAAGCGGAAGATGTATGAGGAATTCCTTAGTAAAGTCTCTATTTTAGAGTCTC  900
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  892   CACTGAGAAAGCGGAAGATGTATGAGGAATTCCTTAGTAAAGTCTCTATTTTAGAGTCTC  951

Query  901   TGGACAAGTGGGAACGTCTTACGGTAGCTGATGCATTGGAACCAGTGCAGTTTGAAGATG  960
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  952   TGGACAAGTGGGAACGTCTTACGGTAGCTGATGCATTGGAACCAGTGCAGTTTGAAGATG  1011

Query  961   GGCAGAAGATTGTGGTGCAGGGAGAACCAGGGGATGAGTTCTTCATTATTTTAGAGGGGT  1020
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  1012  GGCAGAAGATTGTGGTGCAGGGAGAACCAGGGGATGAGTTCTTCATTATTTTAGAGGGGT  1071

Query  1021  CAGCTGCTGTGCTACAACGTCGGTCAGAAAATGAAGAGTTTGTTGAAGTGGGAAGATTGG  1080
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  1072  CAGCTGCTGTGCTACAACGTCGGTCAGAAAATGAAGAGTTTGTTGAAGTGGGAAGATTGG  1131

Query  1081  GGCCTTCTGATTATTTTGGTGAAATTGCACTACTGATGAATCGTCCTCGTGCTGCCACAG  1140
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  1132  GGCCTTCTGATTATTTTGGTGAAATTGCACTACTGATGAATCGTCCTCGTGCTGCCACAG  1191

Query  1141  TTGTTGCTCGTGGCCCCTTGAAGTGCGTTAAGCTGGACCGACCTAGATTTGAACGTGTTC  1200
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  1192  TTGTTGCTCGTGGCCCCTTGAAGTGCGTTAAGCTGGACCGACCTAGATTTGAACGTGTTC  1251

Query  1201  TTGGCCCATGCTCAGACATCCTCAAACGAAACATCCAGCAGTACAACAGTTTTGTGTCAC  1260
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  1252  TTGGCCCATGCTCAGACATCCTCAAACGAAACATCCAGCAGTACAACAGTTTTGTGTCAC  1311