Sequence
atgc intronic sequence ATGC exonic sequence...agttgaaactgatgaaagaaatagccctgttttgcactgtgaatagaagccctgtttcaattccgtcccaaaaatctgattcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCGTGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G062042_T02 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 25
agttgaaactgatgaaagaaatagccctgttttgcactgtgaatagaagccctgtttcaattccgtcccaaaaatctgattcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCGTGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG
||| || ||| || ||| | | ||| || | | | || ||||||||| | || ||| | | || | |||| ||||||||||||||||||||||||||||||||| ||||||||||||||||| |||||||||||||| ||||||||||| |||||||| |||||||| ||||| |
gtttgtttcttatggcagg----gccttctattggtctatcagtttt-gctctgtttcaaa---attttgaa---ctg--tttaattattatttgtacagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAACAATGTCTCTGCTGTGAATGAAGCTTTGAATGAGCTTTATGTTGAAGAGG
upper sequence: GRMZM2G062042_T02 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 25
agttgaaactgatgaaagaaatagccctgttttgcactgtgaatagaagccctgtttcaattccgtcccaaaaatctga---ttcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCGTGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG
||| || ||| || ||| | | ||| || | | | | ||||| ||||| | ||| | | || |||||| ||||||||||||||||||||||||||||||||| ||||||||||||||||| |||||||||||||| ||||||||| | |||||||| |||||||| ||||| |
gtttgtttcttatggcagg----gccttctattggtctatcagt------------tttgctccgtttcaaaattttgaactatttcattattctttgtacagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAACAATGTCTCTGCTGTGAATGAATCTTTGAATGAGCTTTATGTTGAAGAGG
upper sequence: GRMZM2G062042_T02 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 25
--------------------agttgaaactgatgaaagaaatagccctgttttgcactgtgaatagaagccct--gtttcaattccgtcccaaaa--atctgattcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCGTGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG
| | || || | | | | | ||| | | | | | | | | | | |||| || || | | || | |||| | ||| |||||||| || | | || || || || |||||||||||||| || |||||||| ||||| || ||||| || ||||||||| |||||| || || |
gtctgcaattttcataccctattgtcaaatgcctacggtttcaatcttatttggtgagataacttgctggctttaaatgctattcagtaataatattgtttgttgcttgg-attttttattcagGCTGGCCACCTCAGATTAGTTAAGCCGTACATGGTTGCAGTTCAAAGCAACAATGTGTCTGCTGTCAATGAGGCTTTGAATGAAATTTATGCTGAGGAAG
upper sequence: GRMZM2G062042_T02 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 25
agttgaaactgatgaaagaaatagccctgttttgcactgtgaatagaagccctgtttcaattccgtcccaaaaatctgattcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCGTGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG
| | | | || | || | | | | | || || || ||| | || |||| | |||||||||| | | |||||||||||||||||||||||||||||| || ||||| || ||||| || |||||||| |||||||| | ||||| || || |
--gtaggatcattagtggtaaaaatttaattagatattagttgttg----catgccataactctaatgggaaacttcactttaatatgct------atagGCTGGTCACCTCCGTCTTGTGAAACCATATATGGTTGCAGTTCAAAGCAACAACGTATCTGCTGTTAATGAAGCGTTGAATGAGATATATGTTGAGGAGG
upper sequence: GRMZM2G062042_T02 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 24
agttgaaactgatgaaagaaatagccctgttttgcactgtgaatagaagccctgtttcaattccgtcccaaaaatctgattcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCGTGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG
| | | || || | | || | | | | || |||| ||| | | | ||| | | | ||| || | |||||||||| | | |||||| || ||||| |||||||||||||||||||||||||| ||||| || ||||||||| | |||||| | ||||| || || |
--gtagcattaatactgtcaacaatttcatcttaatttttactttataacctgttttccatttcactctatgaatattttccctgtgatgtatt--atagGCTGGTCATCTCCGTCTTGTCAAGCCATACATGGTTGCAGTTCAGAGTAACAATGTGTCTGCTGTTAATGAAGCCCTTAATGAAATATATGTTGAGGAGG
upper sequence: GRMZM2G062042_T02 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 25
agttgaaactgatgaaagaaatagccctgttttgcactgtgaatagaagccctgtttcaattccgtcccaaaaatctgat-tcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCGTGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG
| || | || | | || || | ||| || |||| || | || | || ||| || | | ||| | | | |||||||||| | | |||||||||||| |||||| |||||||||| || |||||||| ||||| || |||||||| |||||||| | |||||||| || |
---------gtaggatgaatattggcaaaaatttcatt--agatatcagt--tgttgca-tgccataacactaatgggaaatttcattgatatgct-atagGCTGGTCACCTCCGTCTTGTGAAACCGTATATGATTGCAGTTCAAAGCAACAATGTATCTGCTGTTAATGAAGCGTTGAATGAGATATATGTCGAGGAGG
upper sequence: GRMZM2G062042_T02 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 23
------------------agttgaaactgatgaaagaaatagccctgttttgcactgtgaatagaagccctgtttcaa----ttccgtcccaaaa----atctgattcttgttgctctttggac---agGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCGTGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG
| || | || ||| || | | ||||| ||||| || |||||| || || | | | | || || | |||| | | | ||| ||||||| || | | | || || || || ||||||||||||| || || ||||| ||||| || |||||||| ||||||||| ||||||| || || |
gtctgtaggtctcattctattttctaatgtgttaagttttaatcttcttttg----gtgaagttaataactgtttgaaaatattttatgcaatattcttatttgttgcttgattttttctggtttttagGCTGGCCACATCCGATTGGTTAAGCCGTACTTGGTTGCAGTTCAAAGCAATAATGTGTCTGCTGTTAATGAAGCTTTGAATGAAATTTATGTTGAGGAGG
upper sequence: GRMZM2G062042_T02 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 24
agttgaaactgatgaaagaaatagccctgttttgcactgtgaatagaagccctgtttcaattccgtcccaaaaatctgattcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCGTGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG
| | | || || | |||| | | | | || |||| ||| | | | ||| | | | ||| || | |||||||||| | | |||||| || || || ||||||||||||||||||||||| || ||||| || ||||||||| |||||||| | ||||| || || |
--gtagcattaatactgtcaacaatttcattttagtttttactttataacctgttttccatttca-ctgatgaatattttccctgtgatgtatt--atagGCTGGTCATCTCCGTCTTGTCAAGCCTTACATGGTTGCAGTTCAGAGTAACAACGTGTCTGCTGTTAATGAAGCCCTGAATGAAATATATGTTGAGGAGG
upper sequence: GRMZM2G062042_T02 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 25
-------------------agttgaaactgatgaaagaaatagccctgttttgcactgtgaatagaagccct--gtttcaattccgtcccaaaa--atctgattcttgttgctctt-tggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCGTGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG
| | || || | || | | | ||| | | | | | | | | | |||| || | | | || | |||| | || | |||||||| || | | || || || || |||||||||||||| || |||||||| || || || |||||||| ||||||||| ||||||| || || |
gtctgcaatttcataccctattgccaaatggctacagtttcaatcttatttggagagataatttgctggtttcaaatgctattctgtaatagtattgtttgttgcttggattttttattttcagGCTGGCCACCTTAGATTAGTTAAGCCGTACATGGTTGCAGTTCAAAGCAACAATGTGTCCGCTGTCAATGAAGCTTTGAATGAAATTTATGTTGAGGAAG
upper sequence: GRMZM2G062042_T02 (Zea mays), 3'ss of exon 10
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 25
agttgaaactgatgaaagaaatagccctgttttgcactgtgaatagaagccctgtttcaattccgtcccaaaaatctgattcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCGTGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG
| ||| |||| || | |||||| || | || | | | | | || | | || ||| || || | || ||| ||||||||||| |||| |||| | || ||||| ||| ||||||||||||| |||||||||||||| || ||||| || ||||||| | || || ||||| |
gttagaagctgac-----tgatgactttgtttttttctataaa-aacaactgagctacattact----taacaat-tggtttcttctgatct-----cagGCTGGTCACTTGCGTCTTATCAAGCCATACATGATTGCAGTTCAGAGCAACAATGTCTCTGCTGTTAATGAGGCTCTGAATGAGATATACGTGGAAGAAG
upper sequence: GRMZM2G062042_T02 (Zea mays), 3'ss of exon 10
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 25
agttgaaactgatgaaagaaatagccctgttttgcactgtgaa--tagaagccctgtttcaat--tccgtcccaaaaatctgattcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCGTGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG
| || |||| | || || | |||| | || || | | || | || || | | | | |||||||| || | ||||||||||| |||| ||| | || ||||||||||||||||||||||| || ||||| ||||| || |||||||| ||||||| | |||| ||||| |
gttagaggctgaccattgatttaa---tattttctgttaaaaacttatcaccagtggcttaacaatctatatctgatgattatttcttgtttctgatc--tcagGCTGGTCACTTGCGCCTTATTAAGCCATATATGGTTGCAGTTCAGAGCAATAATGTATCTGCTGTAAATGAAGCTCTGAATGAGATATATGCAGAAGAAG
upper sequence: GRMZM2G062042_T02 (Zea mays), 3'ss of exon 10
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 25
------------agttgaaactgatgaaagaaatagccctgt------tttgcactgtgaatagaagccct---gtttcaa-----ttccgtcccaaaaatctgattcttgttg-ctctttgga---cagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCGTGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG
|| | ||| | ||| |||| || | || ||| | | | |||| || || ||| |||| || ||| | |||||||| ||||||||||| | ||||||||||| || ||||||||||| |||||||||| ||||| |||| || |||||||| || |||| || |||| || || |
gtctgcatgtttgcttactctttatgtgatggatattgctgtgtgcttcttttagtgggaacaaatgattaaaagtttaaaaatggttttgtcaatggtatcttatgcttatgatctctttgggtttcagGCTGGTCACCTTCATCTTGTGAAGCCCTATATGGTTGCTGTTCAGAGTACTAATGTGGCTGCGGTAAATGAAGCATTAAATGGTATTCATGTAGAGGAGG
upper sequence: GRMZM2G062042_T02 (Zea mays), 3'ss of exon 10
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 25
-----agttgaaactgatgaaagaaatagccctgttttgcactgtgaatagaagccctgtttcaatt-ccgtcccaaaaatctg---attctt----------gttgctctttgga---cagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCGTGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG
||| ||| | | | || | | | || | |||||| | | | | | | | | | |||| ||| | ||||| ||||| ||||| | ||||||||||| |||||||||||||||||||||||||||||||| ||||| |||||||| || ||||||| ||||||| || || |
gtttttgtttgtgctggcttttttgtttcctttcttcttcttctgaagtatgttacttgtttccttgactcttctagacgtttatgtactcttttggttatgcgttttttgttggattccagGCAGGTCACCTTCATCTTGTGAAGCCATATATGGTTGCAGTTCAGAGTAACAATGTTTCTGCTGTGAATGAGGCTTTGAATGGGATTTATGTTGAGGAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaagccctgtttcaattccgtcccaaaaatctgattcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCGTGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG
atctgat putative branch site (score: 4)
ttcttgttgctcttt CT-rich tract
tttcaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agttgaaactgatgaaagaaatagccctgttttgcactgtgaatagaagccctgtttcaattccgtcccaaaaatctgattcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCGTGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - ctgatga
- - - - - - - -aagaaata
- - - - - - - - - - - - - -tgttttg
- - - - - - - - - - - - - - - - - - - - gaatagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgattc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgct