Sequence
atgc intronic sequence ATGC exonic sequencegtaatatgtttctccacattttagtgatattttggtggaaaaaatggaagatgacatttgacatgatcacatgaaccttgtgtgcacgaactcactgttacccatgtttcagGTAATTGACAAGTCATTTGGTTTCGACACAGCAGTTGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAAGCTGTAAGTGCTGAGAATGGTATAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os06g05860.1 (Oryza sativa), 3'ss of exon 8
gtaatatgtttctccacattttagtgatattttggtggaaaaaatggaagatgacatttgacatgatcacatgaaccttgtgtgcacgaactcactgttacccatgtttcagGTAATTGACAAGTCATTTGGTTTCGACACAGCAGTTGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAAGCTGTAAGTGCTGAGAATGGTATAG
||||| || | |||||| || ||| ||| ||| || |||| | | |||| || | | ||||| | ||||||||||||| ||||||||||||||||| |||||||||||||| |||||||||||||||||||||||||| ||||||| ||| || |||||||||||||
gtaatgatctttttcacattatattgacattagggtatgaattatggtg-----------------------------tatatgcat-aatttgtttctaccctatgtgcagGTAATTGACAGATCATTTGGTTTCGACACTGCAGTTGAGGAGGCCCAACGTGCAATAAATGCTGCTCATGTAGAAGCTGGAAGCGCCGAGAATGGTATAG
upper sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA07G15170.1 (Glycine max), 3'ss of exon 8
gtaatatgtttctccacattttagtgatattttggtggaaaaaatggaagatgacatttgacatgatcacatgaaccttgtgtgcacgaactcactgttacccatgtttcagGTAATTGACAAGTCATTTGGTTTCGACACAGCAGTTGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAAGCTGTAAGTGCTGAGAATGGTATAG
|||| | || | | | || ||| | || | || | ||| | || | | ||| ||| || | | | |||| ||||| ||||| ||||| || ||||| || ||||||||||||||||| || |||||||| || ||||| ||||||| ||||| ||| ||||| ||||
gtaaggttttattttcttctacattgtggctttaaactcataatttaaaccccattagcatcattgattggtaaatttcttctgc--tgtctctttgatgcttaa----tagGTTATTGATAAGTCCTTTGGCTTTGACACTGCTGTTGAGGAGGCTCAACGAGCTATAAATGCAGCACATGTTGAAGCTGAAAGTGTTGAAAATGGCATAG
upper sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA07G01710.1 (Glycine max), 3'ss of exon 7
gtaa-tatgtttct-ccacattttagtgatattttggtggaaaaaatggaagatgacatttgacatgatcacatgaaccttgtgtgcacgaactcac--tgttacccatgtttcagGTAATTGACAAGTCATTTGGTTTCGACACAGCAGTTGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAAGCTGTAAGTGCTGAGAATGGTATAG
|| | ||| || | | | || | ||| | | || | | | | | ||| | || | || |||| | || |||||| ||||| |||||||||||||| ||||| || ||||| ||||| ||||| || ||||||||||||||||||||||| | ||| ||||||||||||| |
gtgagcatgcttgaattggacatctgaagccttacaatagaagctactttgctgaaaatataaaaaggatttacttttaaactgtcacctaattaaccatgttgtacctgaatcagGTTATTGATAAGTCATTTGGTTTTGACACTGCTGTTGAAGAGGCACAACGAGCCATAAATGCTGCTCATGTGGAAGCAGAAAGCACTGAGAATGGTATTG
upper sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA08G03570.1 (Glycine max), 3'ss of exon 8
gtaatatgtttctccacattttagtgatattttggtggaaaaaatggaagatgacatttgacatgatcac-atgaaccttgtgtgcacgaactcactgttacccatgtttca---gGTAATTGACAAGTCATTTGGTTTCGACACAGCAGTTGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAAGCTGTAAGTGCTGAGAATGGTATAG
| | | |||| | | | | | |||| ||| | ||| |||| | ||| | | | |||| | || | | ||| ||||| ||||| || || || |||||||| |||||||||||||||||||| |||||||| || ||||| || |||| ||||| ||| ||||| ||||
---------------gtacatcatggatag--cagctcttccatttattgct--tatttcccattagcaccatgagct---tgtaaaatggtttaatgttctctctggcttaatagGTTATTGATAAGTCCTTCGGCTTTGACACAGCTGTTGAGGAGGCTCAACGTGCTATAAATGCAGCACATGTTGAGGCTGAAAGTGGTGAAAATGGCATAG
upper sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA04G09180.1 (Glycine max), 3'ss of exon 8
-----------------gtaatatgttt-ctccacattttagtgatattttggtggaaaaaatggaagatgacatttgacatgatcacatgaaccttgtgtgcacgaactcactgttacccatgt-ttcagGTAATTGACAAGTCATTTGGTTTCGACACAGCAGTTGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAAGCTGTAAGTGCTGAGAATGGTATAG
|| |||| ||| | | | | | || | | | ||||| | ||| | | | | | | | | | || | | | ||| | | | || |||| |||||||| || |||||||| || || || |||||||||||||||||||| || ||||| |||||||| ||||||| |||| |||||||||||| |
gtatgcttgttcacaatgtcatatttttgtttctccctggaactctaatcttatcattaaaatatatc-tgaagtgttagttctctatgaggaaacttcat-catgttcggattgtcttctttttctttagGTTATTGACAAATCTTTTGGTTTTGATACTGCGGTTGAGGAGGCTCAACGTGCCATTAATGCAGCTCATGTTGAAGCTGAAAGTATTGAGAATGGTATTG
upper sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA13G42990.1 (Glycine max), 3'ss of exon 8
-----------------gtaatat-gtttctccacattttagtgatattttggtggaaaaa-atggaagatgacatttgacatgatcacatgaaccttgtgtgcacgaactcactgttacccatgtttcagGTAATTGACAAGTCATTTGGTTTCGACACAGCAGTTGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAAGCTGTAAGTGCTGAGAATGGTATAG
|||| || || | | | || || ||| ||| || | | | | | || | || ||| | | | | | ||| | | || | |||| |||||||||||| ||||||||||||| || ||||| ||||| ||||| ||||| ||| |||||||||||||||| | ||| ||||||||||| || |
gtaatgatgctttagttgtaaaattgtatatgtgaaaatt-gttatacttttatgctatcatactccaaaggaaaaaggatttgag-attaaagtgtcacctatttaatgtcatt-ctgtatttgaattagGTTATTGACAAGTCAATTGGTTTCGACACTGCTGTTGAAGAGGCACAACGAGCAATCAATTCTGCTCATGTGGAAGCAGAAAGCGCTGAGAATGGAATTG
upper sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA01G00870.2 (Glycine max), 3'ss of exon 5
gtaatatgtttctccacattttagtgatattttggtggaaaaaatggaagatgacatttgacatgatcacatgaaccttgtgtgcacgaactcactgttacccatgtttcagGTAATTGACAAGTCATTTGGTTTCGACACAGCAGTTGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAAGCTGTAAGTGCTGAGAATGGTATAG
|||| | ||| | | | | | | || | ||| || | || ||| || | || | | | | |||| | | |||| ||||| ||||| ||||| || ||||| || ||||||||||||||||| || |||||||| || ||||| ||||||| ||||| || ||||| ||||
gtaagttttttttttccttctacattgtggctttaaactcataatttaaacc--ccattagcatcattaattggtaaatttcttc-------tgctgtctcttgcttaatagGTTATTGATAAGTCTTTTGGCTTTGACACTGCTGTTGAGGAGGCTCAACGAGCTATAAATGCAGCACATGTTGAAGCTGAAAGTGTAGAAAATGGCATAG
upper sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA05G36050.1 (Glycine max), 3'ss of exon 8
gtaatatgtttctccacattttagtgatattttggtggaaaaaatggaagatgacatttgacatgatcacatgaaccttgtgtgcacgaactcactgttacccatgtttcagGTAATTGACAAGTCATTTGGTTTCGACACAGCAGTTGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAAGCTGTAAGTGCTGAGAATGGTATAG
||| || || ||| |||| ||| | | || ||||| | | || || | ||| | | |||| ||||| ||||| || || || |||||||| |||||||||||||||||||| |||||||| || ||||| || |||| ||||| ||| ||||| ||||
gtacatctcttttctgtccattatcaatatcatggatagcagctcttgcattagcac----catgaacttgtaaa----atggtttaatgcatgttgtctctggcttaatagGTTATTGATAAGTCCTTCGGCTTTGACACAGCTGTTGAGGAGGCTCAACGTGCTATAAATGCAGCACATGTTGAGGCTGAAAGTGGTGAAAATGGCATAG
upper sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA08G21370.1 (Glycine max), 3'ss of exon 7
gtaa-tatgtttct-ccacattttagtgatattttggtggaaaaaa--tggaagatgacatttgacatgatcacatgaaccttgt--gtgcacgaactcac--tgttacccatgtttcagGTAATTGACAAGTCATTTGGTTTCGACACAGCAGTTGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAAGCTGTAAGTGCTGAGAATGGTATAG
|||| ||| || | | | || | ||| | | || || | | | | | | || | || | || | || |||| | || |||||| || || |||||||| ||||| ||||| || ||||| ||||| ||||| || ||||||||||||||||||||||| | ||| ||||||||||||| |
gtaagcatgcttgaattggacatccgaagccttacaatagaagctactttgatgagaatgta-aaaacaacgatatacttttaaacagtcacctaattaaccatgttgtacctgaatcagGTTATCGATAAGTCATTCGGTTTTGACACTGCTGTTGAAGAGGCACAACGAGCCATAAATGCTGCTCATGTGGAAGCAGAAAGCACTGAGAATGGTATCG
upper sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA15G02400.1 (Glycine max), 3'ss of exon 8
--------------------gtaatatgtttctccacattttagtgatattttggtggaaaaaatggaagatgacatttgacatgatcacatgaaccttgtgtgcacgaactcactgttacccatgtttcagGTAATTGACAAGTCATTTGGTTTCGACACAGCAGTTGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAAGCTGTAAGTGCTGAGAATGGTATAG
| | | | | | | ||| | | || || | | ||| | | | ||| | | | | | ||| | | || || |||| |||||||| ||| ||||||||||||| || ||||| ||||| ||||| ||||| ||| |||||||||||||||| | ||| || |||||||| || |
gtaatgatgctttagttgtaaaattgtatatgtggaaattgctatacttttatgccatcgtactcgaaaggaaaaaaagaatttgagttta-aagtgtcacctatttaatgtcatt-ctgtatttgatttagGTTATTGACAAATCAATTGGTTTCGACACTGCTGTTGAAGAGGCACAACGAGCAATCAATTCTGCTCATGTGGAAGCAGAAAGCGCGGAGAATGGAATTG
upper sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA06G09320.1 (Glycine max), 3'ss of exon 7
-----------------gtaatatgtttc--tccacattttagtgatattttggtggaaaaaatggaagatgacatttgacatgatcacatgaaccttgtgtgcacgaactcactgttacccatgtttcagGTAATTGACAAGTCATTTGGTTTCGACACAGCAGTTGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAAGCTGTAAGTGCTGAGAATGGTATAG
|| |||| ||| ||| | | | || | | | ||||| | ||| | | | | | | || || | | || | | || |||| |||||||| || |||||||| || || || |||||||||||||||||||| || ||||| |||||||| ||||||| |||| ||||||||| || |
gtatgcttgttcacaatgtcatattttttgttcctccctggaactctaatcttatcattaaaatacatt-tgaagtgttggttatctatgaagaaacttcatgttcggattgccttct---ttttctttagGTTATTGACAAATCTTTTGGTTTTGATACTGCGGTTGAGGAGGCTCAACGTGCCATTAATGCAGCTCATGTTGAAGCTGAAAGTATTGAGAATGGCATTG
upper sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 8
lower sequence: AT4G32840.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaatatgtttctccacattttagtgatattttggtggaaaa--aatggaagatgacatt-tgacatgatcacatgaaccttgtgtgcacgaactcactgttacccatgtttcagGTAATTGACAAGTCATTTGGTTTCGACACAGCAGTTGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAAGCTGTAAGTGCTGAGAATGGTATAG
|||| | | |||| | || | | || || | ||| || | || || ||| || | | || | || | || | |||| ||||||||||| ||||| || || || || |||||||||||||||||||| || ||||| || ||||| ||||| |||| || || || || |
gtaagtcctagattatcattattgtagtctgcactctcaaccttaacctcctctcctattctggttagttcgcaagaagctcaatttgatga------tagtatctctgatctagGTCATTGACAAGTCCTTTGGATTTGATACTGCGGTTGAGGAGGCTCAACGTGCTATTAATGCAGCGCATGTTGAAGCGACCAGTGTGGAAAACGGCATTG
upper sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 8
lower sequence: Vv11s0016g02850.t01 (Vitis vinifera), 3'ss of exon 8
----------------------------------------gtaatatgtttctccacattt-tagtgatattttggtggaaaaaatggaagatgacatttgacatgatcacatgaaccttgtgtgcacga-----actcactgttacccatgtttcagGTAATTGACAAGTCATTTGGTTTCGACACAGCAGTTGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAAGCTGTAAGTGCTGAGAATGGTATAG
|| || || | || |||| | | | | ||||| | | | | | | || | | | | || || | || || | ||||| ||||||||||| ||||| || ||||| || ||||||||||| |||||||| || ||||| || ||||| ||| ||| |||| |||||| |||| |
gtacatctctttgtttccttaattgctgattataggaccggttggatattacacctgatttattgcatagatataaattcaaaaacaatttttttcctattttttattgaccaattctctttttagttgatttttacctccgactattgctggtacagGTTATTGACAAGTCCTTTGGCTTTGACACTGCTGTTGAGGAGGCCCAACGTGCTATTAATGCAGCACATGTTGAATCTGAAAGTATCGAGAATTGTATTG
upper sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 8
lower sequence: PP1S131_40V6.1 (Physcomitrella patens), 3'ss of exon 8
--------------------------------------------------gtaa-tatgtttct-----ccacattttagtgatattttggtggaaaaaatggaagatgacat--ttgaca------tgatcacatgaa--ccttgtgtgca-----cgaactcactgttaccca------tgtttcagGTAA-------TTGACAAGTCATTTGGTTTCGACACAGCAGTTGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAAGCTGTAAGTGCTGAGAATGGTATAG
|||| || ||||| | | ||| | | | | | | ||| | | ||||||||| || | || | | |||| || |||||| | || || || | | | ||| |||||| | || |||||||| || || || |||||||| || || ||||| |||||||| ||||| |||||||||||||||| |||| | |||||||| | |
gtacgtcactgtcttttgatatacacttggtaggattacgtgcggtagaagtaactaagtttcaggaagctaatatttggatacgtgtgtgcgcaaagactaccagatgacatgattaattatgtattgttttcttgaagtccaagtgtgccaccgtctaatgcatatttgtcgaatgtggtatttgaggtaacagGTCATAGATAAGTCATTCGGATTTGATACAGCAGTGGAAGAAGCTCAGCGTGCAATCAATGCAGCTCATGTGGAAGCTGAGAGTGTTCAGAATGGTCTTG
upper sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 8
lower sequence: PP1S69_13V6.1 (Physcomitrella patens), 3'ss of exon 8
gtaatatgtttct-------ccacattttagtgatattttggtggaaaaaatggaagatgacatttgacatgatcacatgaacc--ttg--tgtgcacgaactcactgttacccatgtttc--------------agGTAATTGACAAGTCATTTGGTTTCGACACAGCAGTTGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAAGCTGTAAGTGCTGAGAATGGTATAG
||||| || | || | ||| || | | | |||| | | | | | || | |||||| | | | || ||| | | | || || | | ||| | || ||||||| ||||| || || |||||||| || || || || || ||||| ||||| ||||| |||||||||||||||| ||| || | |||||| | |
gtaatgtgctccttatagtacaacacttgaatttttttttactacacatgcttgcgtgct-tatgtcgcatgatgatagcatcccgttgcttatatattgacctcctagtccttgggttacttggagatgagagcagATAATTGATAAGTCCTTCGGGTTCGACACTGCCGTGGAAGAAGCACAACGAGCAATCAATGCAGCTCATGTGGAAGCTGAGAGTACTCATAATGGTGTGG
upper sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 8
lower sequence: PP1S81_165V6.4 (Physcomitrella patens), 3'ss of exon 9
-------------------gtaatatgtttctccacattttagtgatattttggtggaaaaaatggaagatgacatttgacat-gatcacatgaaccttgtg-tgcacgaactcactgttacccatgtttcagGTAATTGACAAGTCATTTGGTTTCGACACAGCAGTTGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAAGCTGTAAGTGCTGAGAATGGTATAG
| | | | || || | ||| |||| ||| | | | | | | | | | | | || | | | || | | | | | ||||| || ||||| ||||||||||| || || |||||||| || || || |||||||| |||||||| || |||||||||| |||| | | ||||| || |
gtacgttttagacacggaaattcaacaacacgatggaattctctg-tttttcaatggattgaattgtgtgggtttctgattgtaggttaagcaacacaagagctgaatggaaaatatggtgcacgtttggcagGTCATAGACAAATCATTTGGTTTTGATACCGCAGTTGAAGAAGCACAGCGTGCAATTAATGCTGCGCACGTGGAAGCTGAGAGTGTTCATAATGGCATTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgacatgatcacatgaaccttgtgtgcacgaactcactgttacccatgtttcagGTAATTGACAAGTCATTTGGTTTCGACACAGCAGTTGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAAGCTGTAAGTGCTGAGAATGGTATAG
aactcac putative branch site (score: 2)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatatgtttctccacattttagtgatattttggtggaaaaaatggaagatgacatttgacatgatcacatgaaccttgtgtgcacgaactcactgttacccatgtttcagGTAATTGACAAGTCATTTGGTTTCGACACAGCAGTTGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAAGCTGTAAGTGCTGAGAATGGTATAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG