Sequence
atgc intronic sequence ATGC exonic sequence...ttgcatttcctttatgcaatatatttggttggaaaaatggtgtttagcataaacatttttgattttgatggatttgttactatgttttcatcaatgacagGATAATAAAGATGCTCGTCATGTTAAAACATATGAGGTTGCACTGAAGGATAAAGATTTTGTTGAAGGTCCATGGTCCCAGAACAATCTCGATAATGGGG
Basic information
species | Glycine max |
transcript | GLYMA08G13680.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G13680.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G402002_T01 (Zea mays), 3'ss of exon 8
-------------------ttgcatttccttta-tgcaatatatttggttggaaaaatggtgtttagcataaacattt-----ttgattttgatggatttgttactatgttttcatcaatg--acagGATAATAAAGATGCTCGTCATGTTAAAACATATGAGGTTGCACTGAAGGATAAAGATTTTGTTGAAGGTCCATGGTCCCAGAACAATCTCGATAATGGGG
| | | ||||| | || | |||| || | ||| | || | | ||| ||||| | | || || || | || | |||||||||||||||| | |||||||| || ||||| |||||||||||||| |||||||||||||| ||||| ||||||||||| ||| | |||||||| |
gtttgtttacacttcttgatgacctcacctttgctagaagagttttgaacaattgaactgcattttgttatgacttgtgatagttgtttttgtttatatgatttgcatcttatgctctacacttcagGATAATAAAGATGTGAGGCATGTTAAGACTTATGAAGTTGCACTGAAGGACAAAGATTTTGTTGAGGGTCCTTGGTCCCAGAATAATGTAGATAATGGTG
upper sequence: GLYMA08G13680.1 (Glycine max), 3'ss of exon 8
lower sequence: AT4G05420.1 (Arabidopsis thaliana), 3'ss of exon 8
-ttgcatttcctttatgcaatatatttggttggaaaaatggtgtttagcataaacatttttgattttgatggatttgttactatgttttcatcaatgac--agGATAATAAAGATGCTCGTCATGTTAAAACATATGAGGTTGCACTGAAGGATAAAGATTTTGTTGAAGGTCCATGGTCCCAGAACAATCTCGATAATGGGG
|| || |||||| |||||| | | || ||| || | | | ||| || || |||| | |||| | |||| || ||||||||||||||||| ||||||||||| || | || || ||||| |||||||| || ||||||||||| ||||||| |||||| ||||| |
ttttttttaactttataatctatattgatgatgtagtctgttgtacgagatgcaatctagaggtttctccgg---tgggactaactaatcattggttgtgtagGACAACAAAGATGCTCGTCATGTCAAAACATATGAAGTCTCTCTTAAAGATAAGGATTTTGTCGAGGGTCCATGGTCTCAGAACAGTCTCGACAATGGTG
upper sequence: GLYMA08G13680.1 (Glycine max), 3'ss of exon 8
lower sequence: AT4G21100.1 (Arabidopsis thaliana), 3'ss of exon 8
---ttgcatttcctttatgcaatatat-ttggttgg----aaaaatggtgtttagcataaacatttttgattttgatggatttgttactatgttttcatcaatgacagGATAATAAAGATGCTCGTCATGTTAAAACATATGAGGTTGCACTGAAGGATAAAGATTTTGTTGAAGGTCCATGGTCCCAGAACAATCTCGATAATGGGG
|| |||| | || | | ||| |||||| |||| | | || || || |||| | | || | | ||| ||| || | | |||||| || ||||||||||||||||| ||||||||||| ||| | || |||||||| | ||||| |||||||||||||| |||||||||||||| ||||| |
ctgctgtattttttaaataaattgtatcttggtttactttgctaatgcaatgt-gctcaaggatgtttg--ctgggtgaactaatta--atgcttgggt---ttacagGACAACAAAGATGCTCGTCATGTCAAAACATATGAAGTTTCTCTAAAGGATAAGAACTTTGTCGAAGGTCCATGGTCACAGAACAATCTCGACAATGGTG
upper sequence: GLYMA08G13680.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv10s0003g04360.t01 (Vitis vinifera), 3'ss of exon 8
---ttgcatttcctttatgcaatatatttggttggaaaaatggtgt-ttagcataaacatttttgattttgatggatttgttactatgttttcatc--aatgacagGATAATAAAGATGCTCGTCATGTTAAAACATATGAGGTTGCACTGAAGGATAAAGATTTTGTTGAAGGTCCATGGTCCCAGAACAATCTCGATAATGGGG
|| || || || | ||| || | | | ||| |||| | || | | | ||||| | | | | || || ||| |||||||| |||||||| ||||||||||||||||||||||| || |||||||||| ||||||||||| ||||| ||| | ||||||||||| || |||||||
aacttagatggccccactgtgttccattatgtagcatcagaagtgcattaggaagaata------actcagatggcctcaccatgttctcttgattcaaattgcagGATAACAAAGATGCACGTCATGTTAAAACATATGAGGTGGCTTTGAAGGATAAGGATTTTGTTGAGGGTCCTTGGGCTCAGAACAATCTAGACAATGGGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agcataaacatttttgattttgatggatttgttactatgttttcatcaatgacagGATAATAAAGATGCTCGTCATGTTAAAACATATGAGGTTGCACTGAAGGATAAAGATTTTGTTGAAGGTCCATGGTCCCAGAACAATCTCGATAATGGGG
ttttgat putative branch site (score: 4)
ttttcatc putative PPT
aaacatttttgatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgcatttcctttatgcaatatatttggttggaaaaatggtgtttagcataaacatttttgattttgatggatttgttactatgttttcatcaatgacagGATAATAAAGATGCTCGTCATGTTAAAACATATGAGGTTGCACTGAAGGATAAAGATTTTGTTGAAGGTCCATGGTCCCAGAACAATCTCGATAATGGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- gcatttc
- - - - - - tatgcaa
- - - - - - - - - - - - -tggttgg
- - - - - - - - - - - - - - - - - -aatggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggatttg