Sequence
atgc intronic sequence ATGC exonic sequencegtaggatatctgcttttaactgaagtaatatattcattttcaatgtagtcatggcctgtcataggagatcttacaattcattttgttggttatgcagGTGGGCCTACAGTGGATGCTTTCTTTGTACAATAATAAGTTGAATGGCATTTTGGCTGATGAGATGGGTCTTGGCAAGACTGTACAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G163849_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g02290.1 (Oryza sativa), 3'ss of exon 5
gtaggatatctgcttttaactgaa---------gtaatata-ttcattttcaatgtagtcatggcctgtcat---------aggagatcttacaattcattttgttggttat--gcagGTGGGCCTACAGTGGATGCTTTCTTTGTACAATAATAAGTTGAATGGCATTTTGGCTGATGAGATGGGTCTTGGCAAGACTGTACAG
||||| || | | || |||| || | ||||| | || || || | | | || | | | | ||||||| ||||||| ||| ||||||||||| || ||||||||||| ||||||||||||||||||||||| |||||||||||||||||||||||||||||||| ||||||
gtaggccatttaccttcaacttaattttcttatatgatataatatatatttaaaacatttcaagtctatttccaaccaccaaaaaaaatctacaatttgatttgttgcctatccacagGTGGGCCTTCAATGGATGCTTTCCTTGTACAATAATAAGTTGAATGGTATTTTGGCTGATGAGATGGGTCTTGGCAAGACCGTACAG
upper sequence: GRMZM2G163849_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA18G46930.1 (Glycine max), 3'ss of exon 4
gtaggatatctgcttttaactgaagtaatatattcattttcaatgtagtcatggcctgtcataggagatcttaca-attcattttgttggttatgcagGTGGGCCTACAGTGGATGCTTTCTTTGTACAATAATAAGTTGAATGGCATTTTGGCTGATGAGATGGGTCTTGGCAAGACTGTACAG
||||| | ||| ||| | |||| | | | | | | ||| ||| | || || || | ||| ||| |||| || || |||| || | || ||||||||||| ||||| || || || || ||||| |||||||| |||||||||||||||||||| |||||||||
gtaggttg-ctgagtttga-tgaaattgtctgtaattgcttcttgttgtctt---ttggagta--aggttttatggatttgacatgttatttttgaagGTTGGTTTGCAATGGATGCTTTCCTTGTATAACAACAAATTAAATGGAATTTTGGCAGATGAGATGGGTCTTGGCAAAACTGTACAG
upper sequence: GRMZM2G163849_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA16G03950.1 (Glycine max), 3'ss of exon 5
gtaggatatctgcttttaactgaagtaatatattcattttcaatgtagtcatggcctgtcataggagatcttacaattcatt-----ttgttggttatgcagGTGGGCCTACAGTGGATGCTTTCTTTGTACAATAATAAGTTGAATGGCATTTTGGCTGATGAGATGGGTCTTGGCAAGACTGTACAG
||||| | || || |||| | || | | || | | ||| ||||| | | | || ||| | || | | || || |||| || | || ||||||||||||||||| || || ||||| ||||| |||||||| |||||||||||||||||||| |||||||||
gtaggttgctacattata--tgaaacagtac-tctttaagtgatttctttatg--ctgtcttgagcaagttttcaagactttgataccttatatttttgaagGTTGGTTTGCAATGGATGCTTTCTTTGTATAACAACAAGTTAAATGGAATTTTGGCGGATGAGATGGGTCTTGGCAAAACTGTACAG
upper sequence: GRMZM2G163849_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA09G39380.1 (Glycine max), 3'ss of exon 6
gtaggatatctgcttttaactgaagtaatatattcattttcaatgtagtcatggcctgtcataggagatcttaca-attcattttgttggttatgcagGTGGGCCTACAGTGGATGCTTTCTTTGTACAATAATAAGTTGAATGGCATTTTGGCTGATGAGATGGGTCTTGGCAAGACTGTACAG
||| | | ||| | || | | | | | | | ||| || || | | | || | ||| ||| |||| || || |||| || | || ||||||||||| ||||| || || || || ||||| |||||||| |||||||||||||||||||| |||||||||
gtacgttgctaagtttga--tggaattgtctgtaattgct---tgttttcttgtcttttagagtaaggttttaaggatttgacatgttatttttgaagGTTGGTTTGCAATGGATGCTTTCCTTGTATAACAACAAATTAAATGGAATTTTGGCAGATGAGATGGGTCTTGGCAAAACTGTACAG
upper sequence: GRMZM2G163849_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA07G07550.1 (Glycine max), 3'ss of exon 4
gtaggatatctgcttttaactgaagtaatatattcattttcaa----tgtagtcatg--gcctgtcataggagatctt--acaattcattttgttgg--ttatgcagGTGGGCCTACAGTGGATGCTTTCTTTGTACAATAATAAGTTGAATGGCATTTTGGCTGATGAGATGGGTCTTGGCAAGACTGTACAG
||||| | || || |||| | | | ||||||| | | | ||| | || || | | || | | || | || || | |||| || | || ||||||||||||||||| || || ||||| ||||| |||||||| ||||||||||||||||| || |||||||||
gtaggttgctacattata--tgaaacagttttcaagttttcaagtgatttctttatgctgtcttcttgagcaagttttcaagactttgatacattatatttttaaagGTTGGTTTGCAATGGATGCTTTCTTTGTATAACAACAAGTTAAATGGAATTTTGGCGGATGAGATGGGTCTTGGTAAAACTGTACAG
upper sequence: GRMZM2G163849_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT2G46020.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaggatatctgcttttaactgaagtaatatattcattttcaatgtagtcatggcctgtcataggagatcttacaattcattttgttg-gttatgcagGTGGGCCTACAGTGGATGCTTTCTTTGTACAATAATAAGTTGAATGGCATTTTGGCTGATGAGATGGGTCTTGGCAAGACTGTACAG
||| || | || | || | || || ||| ||| |||| | || | | | || || || || | | ||||| || |||| |||||||| || ||||| ||||| || || || || || ||||||||||||||||||||||| || ||||| |||
gtatctcctccatctatactctatgttgttgcttttttctcactgt---catgccacgttttgatggtttctaaggttttttgctctgtgccaatcagGTTGGATTACAATGGATGCTATCGTTGTATAATAACAAATTAAACGGGATCTTGGCTGATGAGATGGGTCTTGGAAAAACTGTTCAG
upper sequence: GRMZM2G163849_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv15s0046g02290.t01 (Vitis vinifera), 3'ss of exon 5
gtaggatatctgcttttaactgaagtaatatattcatttt-caatgtagtca--tgg--cctgtcatag--gagatct-tacaattcattttgt-tggttatgcagGTGGGCCTACAGTGGATGCTTTCTTTGTACAATAATAAGTTGAATGGCATTTTGGCTGATGAGATGGGTCTTGGCAAGACTGTACAG
||||| | | || | || || ||||||| | ||| || ||| ||||| || ||| ||| | | || | | || |||||| || | || ||||||||||| |||||||| || || ||||||| |||||||||||||||||||||||||| || |||||||||
gtaggttg-caatattagatacttgtcattctgtcattttgccttgtgttccactggttcctgttggagttgagttctgtgttaacaatggtatgcaatttggcagGTTGGGTTGCAATGGATGCTTTCCTTGTACAACAACAAACTGAATGGAATTTTGGCTGATGAGATGGGTCTTGGGAAAACTGTACAG
upper sequence: GRMZM2G163849_T01 (Zea mays), 3'ss of exon 5
lower sequence: PP1S25_252V6.1 (Physcomitrella patens), 3'ss of exon 7
-------------------------------------------------------------------------------------------------gtaggatatctgcttttaactgaagtaatatattcatt--ttcaatgtagtcatggcctgtcataggag---atcttacaattcattttgttggttatgcagGTGGGCCTACAGTGGATGCTTTCTTTGTACAATAATAAGTTGAATGGCATTTTGGCTGATGAGATGGGTCTTGGCAAGACTGTACAG
| | | | | || | || || | ||| | || |||| | | | | | || | | || | || | |||||||| ||||||||||||| || ||||||||||||| | ||||||| || | || ||||| ||||| || || || || || |||
gtaggtgttggtatttgaattatatctttccctcttaaagttcggccacaacacctttgtagacggcagttgaagtcatgaaatttcgaaaggcaatttcgaacggtttaatgtagaagggctacctctttgagcgattcggaattgtgttggcgtaacgaggaattatgtgttctgaattgcttctgtttttttacagGTGGGTTTACAGTGGATGCTATCATTGTACAATAATAGGCTGAATGGGATACTTGCGGATGAAATGGGACTCGGGAAAACAGTCCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgtagtcatggcctgtcataggagatcttacaattcattttgttggttatgcagGTGGGCCTACAGTGGATGCTTTCTTTGTACAATAATAAGTTGAATGGCATTTTGGCTGATGAGATGGGTCTTGGCAAGACTGTACAG
atcttac putative branch site (score: 3)
ttacaattcatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggatatctgcttttaactgaagtaatatattcattttcaatgtagtcatggcctgtcataggagatcttacaattcattttgttggttatgcagGTGGGCCTACAGTGGATGCTTTCTTTGTACAATAATAAGTTGAATGGCATTTTGGCTGATGAGATGGGTCTTGGCAAGACTGTACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA