Sequence
atgc intronic sequence ATGC exonic sequence...tgttgattttgtgcagagctccacaagaaggaaacttgtgaggctgtgactatcattgagactcctccccttgtcattgtcggacttgtggaatgtgaagACCCCCCGTGGCCTACGAACCCTCAACTCTGTCTGGGCCCAACACCTTAGCGAAGAAGTGCGGAGAAGGTTCTACAAGAACTGGTGCAAGAGCAAGAAGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G361049_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA12G36940.1 (Glycine max), 3'ss of exon 3
------------------------------------------------------------------------------------tgttgattttgtgcagagctccacaagaaggaaacttgtgaggctgtgactatcattgagactcctccccttgtcattgtcggacttgtggaatgtg--aagACCCCCCGTGGCCTACGAACCCTCAACTCTGTCTGGGCCCAACACCTTAGCGAAGAAGTGCGGAGAAGGTTCTACAAGAACTGGTGCAAGAGCAAGAAGA
| | | | || |||||| |||||||| || || ||||| ||||| ||||||||||| |||||||| | || |||| ||| |||||| || || ||||| || ||||||||
atatctccatctgatcaattcttgggctattattttcttttacctttgtggcttgtatgtttcttgctttgtacgtgataacattttatgctgtttgtagAGCTTCACAAGAAAGAGACATGTGAAGCTGTTACTATCATTGAAACTCCTCCATTGGTTGTTGTTGGAGTTGTGGGATATGTTAAGACACCTCGTGGCCT--------------------------------------------------------------------------------------
upper sequence: GRMZM2G361049_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA20G30810.1 (Glycine max), 3'ss of exon 3
-tgttgattttgtgcagagctccacaagaaggaaacttgtgaggctgtgactatcattgagactcctccccttgtc--attgtcggacttgtggaatgtgaagACCCCCCGTGG------CCTACGAACCCTCAACTCTGTCTGGGCCCAACACCTTAGCGAAGAAGTGCGGAGAAGGTTCTACAAGAACTGGTGCAAGAGCAAGAAGA
| | || ||| | || || | || ||| | | | | ||| || | |||| | || | | | | | | || | | | | | | | | || || || | || | || | | | | | | | |||| | | |||| | | |
aagctaatgatgtattgcattctttaact-gtttacatgtaacgttctc-ttattatatactatcctttatctatctaactatataatattttctatatcagAGCTTCACAAGAAGGAAACATGTGAGCCTGTTACAATTATTGAGACCCCTCCAATGGTTATTGTTGGTGTTGTGGGTTATGTGAAAACTC-CCCGTGGTCT------
upper sequence: GRMZM2G361049_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA10G36780.1 (Glycine max), 3'ss of exon 3
------------tgttgattttgtgcagagctccacaagaaggaaacttgtgaggctgtgactatcattgagactcctccccttgtcattgtcggacttgtggaatgtgaagACCCCCCGTGGCCTACGAACCCTCAACTCTGTCTGGGCCCAACACCTTAGCGAAGAAGTGCGGAGAAGGTTCTACAAGAACTGGTGCAAGAGCAAGAAGA
| |||| || | | | || | | ||| | | | | |||||| | || | | | | | | | | | | | | | || || || | || | || | | | | | | | |||| | | |||| | | |
tgaagctaatagtattgaattctttaactattacatgaaactttctcttacttg-ttatagc-atcatttaattatctaactatatttcttttttatatcagAGCTTCACAAGAA---GGAAACTTGTGAGCCTGTTACAATTATTGAGACCCCTCCAATGGTTATTGTTGGTGTTGTGGGTTATGTGAAAACTC-CACGTGGTCT------
upper sequence: GRMZM2G361049_T01 (Zea mays), 3'ss of exon 9
lower sequence: AT1G43170.7 (Arabidopsis thaliana), 3'ss of exon 3
--tgttgattttgtgcagagctccacaagaaggaaacttgtgaggctgtgactatcattgagactcctccccttgtcattgtcggacttgtggaatgtgaagACCCCCCGTGGCCTACGAACCCTCAACTCTGTCTGGGCCCAACACCTTAGCGAAGAAGTGCGGAGAAGGTTCTACAAGAACTGGTGCAAGAGCAAGAAGA
||| ||||| | || | ||||| | || | ||| | | || || ||| || | ||||| | | | | | | || | || | || | | | | | | | | | | | | | ||| | | |
gtaagtgaacttgtgtttt-tttcattctgatttgttttgtggag--gtttttgcgatttaaagtcgtcaactttgtgtttttattgttgtgtagAGCTTCACAAGAAGGAGACATGTGAGGCTGTTACCATCATTGAGACACCTGCTATGGTGGTTGTTGGAGTTGTTGCCTATGTGAAGACTCCTAGAGGTTT-------
upper sequence: GRMZM2G361049_T01 (Zea mays), 3'ss of exon 9
lower sequence: AT1G43170.4 (Arabidopsis thaliana), 3'ss of exon 1
-------------------------------------------------------------------------tgttgattttgtgcagagctccacaagaaggaaacttgtgaggctgtgactatcattgagactcctccccttgtcattgtcggacttgtgga--atgtgaagACCCCCCGTGGCCTACGAACCCTCAACTCTGTCTGGGCCCAACACCTTAGCGAAGAAGTGCGGAGAAGGTTCTACAAGAACTGGTGCAAGAGCAAGAAGA
| || | ||||| |||||| ||||||||||| || ||||||||||| || ||||||||||| ||| | | || |||| ||| |||| | |||||||||| || | || | | | | |
agtgaacttgtgtttttttcattctgatttgttttgtggaggtttttgcgatttaaagtcgtcaactttgtgtttttattgttgtgtagagcttcacaagAAGGAGACATGTGAGGCTGTTACCATCATTGAGACACCTGCTATGGTGGTTGTTGGAGTTGTTGCCTATGTGAAGACTCCTAGAGGTTTGAGGTCTTTGA---------------------------------------------------------------------------
upper sequence: GRMZM2G361049_T01 (Zea mays), 3'ss of exon 9
lower sequence: AT1G61580.1 (Arabidopsis thaliana), 3'ss of exon 3
-----------------------------------------------------------------tgttgattttgt--gcagagctccacaagaaggaaacttgtgaggctgtgactatcattgagactcctccccttgtcattgtcggacttgtgga--atgtgaagACCCCCCGTGGCCTACGAACCCTCAACTCTGTCTGGGCCCAACACCTTAGCGAAGAAGTGCGGAGAAGGTTCTACAAGAACTGGTGCAAGAGCAAGAAGA
| || || |||| |||| || |||||||||||||| ||||| |||||||| ||||||||||| ||||| | || |||| || | || | |||| ||||| || ||||| ||
gtgtgttctcactctcttctcttatcaagtcttaatttttgcatgtggttttgtacttaactttttattaatattgttgacagAACTACACAAGAAGGAAACATGTGAAGCTGTGACGATCATTGAGACACCTCCAATGGTGGTTGTTGGTGTGGTTGGTTATGTAAAGACACCTCGTGGTCT--------------------------------------------------------------------------------------
upper sequence: GRMZM2G361049_T01 (Zea mays), 3'ss of exon 9
lower sequence: EFJ30452 (Selaginella moellendorffii), 3'ss of exon 2
----------------------------------------tgttgattttgtgcagagctccacaagaaggaaacttgtgaggctgtgactatcattgagactcctccccttgtcattgtcggacttgtggaatgtg--aagACCCCCCGTGGCCTACGAACCCTCAACTCTGTCTGGGCCCAACACCTTAGCGAAGAAGTGCGGAGAAGGTTCTACAAGAACTGGTGCAAGAGCAAGAAGA
||| |||| | ||||||||||||||||||| || || ||||||||||| ||||| ||||| || || || | || |||||| | |||| | ||||| || || |||||
gtaagtccgctgttcttcccatttcgagagctaaatttcgcgttcattt-gcccagAGCTCCACAAGAAGGAGACCTGCGAGGCTGTGACCATCATCGAGACACCACCGCTCATTATCGTCGGAGTGGTGGCGTACATTAAGACTCCTCGCGGCCT--------------------------------------------------------------------------------------
upper sequence: GRMZM2G361049_T01 (Zea mays), 3'ss of exon 9
lower sequence: EFJ23085 (Selaginella moellendorffii), 3'ss of exon 2
----------------------------------------tgttgattttgtgcagagctccacaagaaggaaacttgtgaggctgtgactatcattgagactcctccccttgtcattgtcggacttgtggaatgtg--aagACCCCCCGTGGCCTACGAACCCTCAACTCTGTCTGGGCCCAACACCTTAGCGAAGAAGTGCGGAGAAGGTTCTACAAGAACTGGTGCAAGAGCAAGAAGA
||| |||| || ||||||||||||||||||| || || ||||||||||| ||||| ||||| || || || | || |||||| | |||| | ||||| || || |||||
gtaagtccgctgttcttcccatttcgagagctaaatttcgcgttcattt-gtccagAGCTCCACAAGAAGGAGACCTGCGAGGCTGTGACCATCATCGAGACACCACCGCTCATTATCGTCGGAGTGGTGGCGTACATTAAGACTCCTCGCGGCCT-------------------------------------------------------------------------------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgactatcattgagactcctccccttgtcattgtcggacttgtggaatgtgaagACCCCCCGTGGCCTACGAACCCTCAACTCTGTCTGGGCCCAACACCTTAGCGAAGAAGTGCGGAGAAGGTTCTACAAGAACTGGTGCAAGAGCAAGAAGA
tatcatt TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgttgattttgtgcagagctccacaagaaggaaacttgtgaggctgtgactatcattgagactcctccccttgtcattgtcggacttgtggaatgtgaagACCCCCCGTGGCCTACGAACCCTCAACTCTGTCTGGGCCCAACACCTTAGCGAAGAAGTGCGGAGAAGGTTCTACAAGAACTGGTGCAAGAGCAAGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
tgttgat
- - - - -tgtgcag
- - - - - - - - -gctccac
- - - - - - - - - - - - - gaaggaaa
- - - - - - - - - - - - - - - - - - - -gaggctg