Sequence
atgc intronic sequence ATGC exonic sequence...agcacaatatttatttttagtttagataagagttcttcacttcatcccatctttgttggcgtgtttcatctagcttacacataccttttcaaattgacagGGTGTGAATGTCGATGATCTCGAGACAAATCATGTTGTCCTTGTTCATGGAGGTGGCTTCGGGGCATGGTGTTGGTACAAATCCATAGCACTTCTAGAAG
Basic information
species | Glycine max |
transcript | GLYMA08G27210.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G27210.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os07g41230.1 (Oryza sativa), 3'ss of exon 1
-----agcacaatatttatttttagtttagataagagttcttcacttcatcccatctttgttggcgtgtttcatctagcttacacataccttttcaaattgacagGGTGTGAATGTCGATGATCTCGAGACAAATCATGTTGTCCTTGTTCATGGAGGTGGCTTCGGGGCATGGTGTTGGTACAAATCCATAGCACTTCTAGAAG
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ctgatgtttcaatttgtgtttgtcctgttgcataatgttcagt-ctctgttacgtgcatgtaatcactaccacactaaccaaaggaatgcttctgaaa----cagGATTTGAACACTAAAGATCTTGAAACCAACATCATTGTTCTTGTTCATGGAGGAGGTTTTGGTGCTTGGTGTTGGTACAAGACTATAGCACTTCTTGAGG
upper sequence: GLYMA08G27210.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G043579_T01 (Zea mays), 3'ss of exon 1
---agcacaatatttatttttagtttagataagagttcttcacttcatcccatctttgttggcgtgtttcatctagcttacacataccttttcaaattgacagGGTGTGAATGTCGATGATCTCGAGACAAATCATGTTGTCCTTGTTCATGGAGGTGGCTTCGGGGCATGGTGTTGGTACAAATCCATAGCACTTCTAGAAG
|| | | | || | | || | | | || || ||| ||| | ||| | |||| || | | | ||||| | ||||| | ||| | || || || |||| ||||||||||| ||||| ||||| || |||||||||||||| | ||| ||||||| ||||
ttggatactaactcagtaattctagtgtttgagtgctttacaactcttcctgggtttatata---accacattttttttacttatggttcatttatcaaacagGATTTGAATACTAAGGATTTGGAAACCAACGTCATTGTTCTTGTTCATGGTGGTGGATTCGGCGCTTGGTGTTGGTACAAGACTATATCACTTCTCGAAG
upper sequence: GLYMA08G27210.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G29770.1 (Arabidopsis thaliana), 3'ss of exon 1
agcacaatatttatttttagtttagataagagttcttcacttcatcccatctttgttggcgtgtttcatctagcttacacataccttttcaaat------tga-cagGGTGTGAATGTCGATGATCTCGAGACAAATCATGTTGTCCTTGTTCATGGAGGTGGCTTCGGGGCATGGTGTTGGTACAAATCCATAGCACTTCTAGAAG
|| ||||| | | || || | || | ||| || ||| | ||| || | |||| | |||| | | ||| ||||| | || | ||||| | || ||||| ||| |||||||||||||||||||| | || || || ||||||||||| ||| |||| |||||||| || |
-------gatccattttgggataggaaaaaaattggattatacattttattggagttcatattttttctcgaacttaaattctttttttttactgatatttgagtagGGTATAAAGCTAGATGACTTGGAAACAAACCATTTTGTCCTTGTTCATGGAGGTAGTTTTGGCGCTTGGTGTTGGTATAAAACCATTGCACTTCTTGAGG
upper sequence: GLYMA08G27210.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv14s0068g00390.t01 (Vitis vinifera), 3'ss of exon 1
--------agcacaatatttatttttagtttagataagagttcttcacttcatcccatctttgttggcgtgtttcatctagcttacacataccttttcaaattgacagGGTGTGAATGTCGATGATCTCGAGACAAATCATGTTGTCCTTGTTCATGGAGGTGGCTTCGGGGCATGGTGTTGGTACAAATCCATAGCACTTCTAGAAG
|||| | | ||| | | || | || || | ||| | ||| | | || || | | ||| | |||||||| |||||| | |||||||| ||||| || ||| |||||||||| ||||||||||| || || || ||||||||||| ||| | ||||| ||||||||||
caatatgtttattgctattgaatcctagaatgtaaaatatttttttttcgtaagtcattctcattgttgcaccgtttttaact---attttcctct-----ttgacagGATGTGAAGCTTGATGATCTAGAGACCAACCATTTTGTCCTTGTCCATGGAGGTGGTTTTGGTGCTTGGTGTTGGTATAAAACTATAGCGCTTCTAGAAG
upper sequence: GLYMA08G27210.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S9_128V6.1 (Physcomitrella patens), 3'ss of exon 1
agcacaatatttatttttagtttagataagagttcttcacttcatcccatctttgt-tggcg----tgtttcatctagcttacacataccttttcaaattgacagGGTGTGAATGTCGATGATCTCGAGACAAATCATGTTGTCCTTGTTCATGGAGGTGGCTTCGGGGCATGGTGTTGGTACAAATCCATAGCACTTCTAGAAG
| | | | | ||| | | | |||| | | || | | || | | | || || | | | || || | || | | | | | | | || || | | || | ||| | |||||||| |||||| | || |||||||||||||||||||| ||| | | || ||
-gtcaagttcctgcacct-gttggtaccactgatctttggtctcgcatattcgtatgtgacaaaaattctaaatataaatggctga-actccttatatttcagGAAGATTCATGGATGTAAACCTGGAAAGCAGGCACTTCGTCTTGGTTCATGGGGGTGGCCTTGGAGCATGGTGTTGGTACAAATCAATATCTTTGCTGGA-- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cccatctttgttggcgtgtttcatctagcttacacataccttttcaaattgacagGGTGTGAATGTCGATGATCTCGAGACAAATCATGTTGTCCTTGTTCATGGAGGTGGCTTCGGGGCATGGTGTTGGTACAAATCCATAGCACTTCTAGAAG
agcttac putative branch site (score: 3)
ccttttca putative PPT
ttttcaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agcacaatatttatttttagtttagataagagttcttcacttcatcccatctttgttggcgtgtttcatctagcttacacataccttttcaaattgacagGGTGTGAATGTCGATGATCTCGAGACAAATCATGTTGTCCTTGTTCATGGAGGTGGCTTCGGGGCATGGTGTTGGTACAAATCCATAGCACTTCTAGAAG
- - - - - - - - - - - - - - - - -tcttcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcgtgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacatac