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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcattctacctcttccagtgtcttcatcctatgcattggtttgttatctcatttgttctacttttctctttttgtcggctgagtcattattgattgtcttgcagTTTCTAGCAACTGTTTCCCATGAGATTCGGACTCCAATGAATGGTGTTTTAG

Basic information

species Zea mays
transcript GRMZM2G158252_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G158252_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os10g21810.1 (Oryza sativa), 3'ss of exon 7
gttcattctacctcttccagtgtcttcatcctatgcattggtttgtta-tctcatttgt-----tctacttttctctttttgtcggctgagtc-attattgattgtcttgcagTTTCTAGCAACTGTTTCCCATGAGATTCGGACTCCAATGAATGGTGTTTTAG
  || ||||| ||||  ||||||  | ||| | |||  || ||  ||| |||| |   |       | | ||  |||  || || ||| |||  ||  ||| ||  |||||||||||||||||||||||| ||||||||| | |||||||||||||||||  |||
-gtccttctatctctagcagtgttcttatcttttgctatgtttctttagtctcctccatgattgctttccttcttctccttatccgctaagtagatctttgtttaccttgcagTTTCTAGCAACTGTTTCACATGAGATTAGAACTCCAATGAATGGTGTACTAG

upper sequence: GRMZM2G158252_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os10g21810.2 (Oryza sativa), 3'ss of exon 7
gttcattctacctcttccagtgtcttcatcctatgcattggtttgtta-tctcatttgt-----tctacttttctctttttgtcggctgagtc-attattgattgtcttgcagTTTCTAGCAACTGTTTCCCATGAGATTCGGACTCCAATGAATGGTGTTTTAG------------------------------------------------
  || ||||| ||||  ||||||  | ||| | |||  || ||  ||| |||| |   |       | | ||  |||  || || ||| |||  ||  ||| ||  |||||||||||||||||||||||| ||||||||| | |||||||||||||||||  |||                                                
-gtccttctatctctagcagtgttcttatcttttgctatgtttctttagtctcctccatgattgctttccttcttctccttatccgctaagtagatctttgtttaccttgcagTTTCTAGCAACTGTTTCACATGAGATTAGAACTCCAATGAATGGTGTACTAGGTTTGTCCTTTATACTTTGTTTTTAATTATTCTTTTCTATCACATTGA

upper sequence: GRMZM2G158252_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA02G47610.1 (Glycine max), 3'ss of exon 7
gttcattctacctcttccagtgtcttcatcctatgcattggtttgttatctcatttgttctacttttctctttttgtcggctgagtcattattgattgtcttgcagTTTCTAGCAACTGTTTCCCATGAGATTCGGACTCCAATGAATGGTGTTTTAG
      || |  |  | | | ||  | ||  | |  | |   || |||  | |||     || | ||      ||| |  |  ||   |  ||     | ||||||||||| ||||| ||||| ||||||||  ||||||||||||||||||||||||
-----atcaaaattattctgagttctgatagtttataatttctt-ttacttaattaaaattaatatttctaccttgacctccaaggattgctttccctttttgcagTTTCTTGCAACAGTTTCACATGAGATCAGGACTCCAATGAATGGTGTTTTAG

upper sequence: GRMZM2G158252_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA14G01040.1 (Glycine max), 3'ss of exon 5
gttcattctacctcttccagtgtcttcatcctatgcattggtttgttatctcatttgttctacttttctctttttgtcggctgagtcatta--ttgattgtcttgcagTTTCTAGCAACTGTTTCCCATGAGATTCGGACTCCAATGAATGGTGTTTTAG
         |  | || | | ||  | ||  | |  | |   || |||  | |||     || | ||  |   ||| |   | |   |||   ||   | | ||||||||||| || || ||||| || |||||  ||||||||||||| ||||||||||
------caaaattatttctgagttctgatggtttataatttctt-ttacttaattaaaattaatatttccaccttgacc-ttcaacgattgctttcccttttttgcagTTTCTTGCGACAGTTTCACACGAGATCAGGACTCCAATGAACGGTGTTTTAG

upper sequence: GRMZM2G158252_T01 (Zea mays), 3'ss of exon 7
lower sequence: AT5G35750.1 (Arabidopsis thaliana), 3'ss of exon 7
gttcattctacctcttccagtgtcttcatcctatgcattggtttgttatctcatttgttctacttttctctttttgtcggctgagtcattattgattgtcttgcagTTTCTAGCAACTGTTTCCCATGAGATTCGGACTCCAATGAATGGTGTTTTAG
                     ||  || |  | || ||     | |  |||||   | | ||||| | | ||        ||||   | |  |  || | |||||||| |||||||||||||| |||||||| |||||||| |||||||| |||||||
---------------------gtgatctt--tgtgaatca---tatagtctcaaaagctttacttgttttttc------actga---aatgcttcttattttgcagTTCCTAGCAACTGTTTCTCATGAGATACGGACTCCGATGAATGGAGTTTTAG

upper sequence: GRMZM2G158252_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv12s0057g00690.t01 (Vitis vinifera), 3'ss of exon 7
---------------------------------------------------------------------------------------------gttcattctacctcttccagtgtcttcatcctatgcattggtttgttatctcatttgttctacttttctctttttgtcggctgagtcattattgattgtcttgcagTTTCTAGCAACTGTTTCCCATGAGATTCGGACTCCAATGAATGGTGTTTTAG
                                                                                              || ||   |        ||    ||  | ||     ||  ||  ||  | || |     | |     |  |  | ||  || |  |||| ||   | | ||| ||||||| |||||||||||||| || ||  ||||||| ||||||||||||||||
gtgcattttattttggccaagtggatggatggttataaatttgtgactgcaatatctttcctcagaacgaatagtttatcctgaggatttttttttgataggaatatcctgaggaattttcttcttcagctttattcttttccccaataaaatttccaccttgatcatatca-ctaaagcattcttc-ctcttttgtagTTTCTTGCAACTGTTTCCCACGAAATCAGGACTCCGATGAATGGTGTTTTAG

upper sequence: GRMZM2G158252_T01 (Zea mays), 3'ss of exon 7
lower sequence: PP1S50_141V6.1 (Physcomitrella patens), 3'ss of exon 6
gttcattctacctcttccagtgtcttcatcctatgcattggtttgttatctcatttgttctacttttctctttttgtcggctgagtcattattgattgtcttgcagTTTCTAGCAACTGTTTCCCATGAGATTCGGACTCCAATGAATGGTGTTTTAG
 || ||| |   |  |    |   || ||  |||    |    |   |    |        ||         |       | || |  || ||||   |  |||||||  | |||||||| || || ||||||||||||||||||||||||||| |||
-tttattatttattattttat---tttattttattttctcacgtaaaaataaaacaaaataacacacaagcatgaaataac-gacttgttgttgaac-ttgtgcagTTCTTGGCAACTGTGTCTCACGAGATTCGGACTCCAATGAATGGTGTTCTAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 52

TTATGCAACTCTGAACTCCCTTGAAAAGGCTGAACATGATTATAGAGTAATGAGAGAACTTAAAGGACAAGCTGAAGCTGCAGATATAGCAAAATCTCAGgttcattcta ... tgtcttgcagTTTCTAGCAACTGTTTCCCATGAGATTCGGACTCCAATGAATGGTGTTTTAG


Block sizes: 39 (upstream exon), 49 (downstream exon)
Score: 16

TTATGCAACTCTGAACTCCCTTGAAAAGGCTGAACATGATTATAGAGTAATGAGAGAACTTAAAGGACAAGCTGAAGCTGCAGATATAGCAAAATCTCAGgttcattcta ... tgtcttgcagTTTCTAGCAACTGTTTCCCATGAGATTCGGACTCCAATGAATGGTGTTTTAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 24

TTATGCAACTCTGAACTCCCTTGAAAAGGCTGAACATGATTATAGAGTAATGAGAGAACTTAAAGGACAAGCTGAAGCTGCAGATATAGCAAAATCTCAGgttcattcta ... tgtcttgcagTTTCTAGCAACTGTTTCCCATGAGATTCGGACTCCAATGAATGGTGTTTTAG


Block sizes: 36 (upstream exon), 38 (downstream exon)
Score: 23

TTATGCAACTCTGAACTCCCTTGAAAAGGCTGAACATGATTATAGAGTAATGAGAGAACTTAAAGGACAAGCTGAAGCTGCAGATATAGCAAAATCTCAGgttcattcta ... tgtcttgcagTTTCTAGCAACTGTTTCCCATGAGATTCGGACTCCAATGAATGGTGTTTTAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttgttctacttttctctttttgtcggctgagtcattattgattgtcttgcagTTTCTAGCAACTGTTTCCCATGAGATTCGGACTCCAATGAATGGTGTTTTAG
                                      tattgat  putative branch site (score: 23)
                                            ttgtctt  CT-rich tract
                                    attattgatt  TA-rich tract