Sequence
atgc intronic sequence ATGC exonic sequencegtgagtgttcatgagctagatataaatatggtctttatggtcactagttgcttttttggttttttctaacaaactttgcgtgttgcagGTTCATGGTAATGTTTGCTTGGCTAGTGTTGTTGTCACACAAACTTTGGACTGGAAACTCCATGCTTTTGATGTTCTATCAGAGTTTGAAGGGAGTAATG
Basic information
species | Glycine max |
transcript | GLYMA20G36180.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G36180.1 (Glycine max), 3'ss of exon 4
lower sequence: AC218972.3_FGT001 (Zea mays), 3'ss of exon 4
------------gtgagtgttcatgagctagatataaatatggtctttatggtcactagttgcttttttggt--tttttctaacaaactttgcgtgttgcagGTTCATGGTAATGTTTGCTTGGCTAGTGTTGTTGTCACACAAACTTTGGACTGGAAACTCCATGCTTTTGATGTTCTATCAGAGTTTGAAGGGAGTAATG
|| | | | | || || ||| | ||| || | ||| || | | | | | || ||| | |||||||||||||||| |||||||| ||||||||||| |||||||| |||| ||||| || ||||||||||||||||| ||||| ||||| | | |||||
taaatcaaaacaatggggtcttaacacataattagaaagtacaacgctataa--acgatttgattgtcaaatgacctgtttgccatcacttgatcaatatagGTTCATGGTAATGTATGCTTGGCCAGTGTTGTTGTTACACAAACCCTGGATTGGAAGCTTCATGCTTTTGATGTTCTGTCAGAATTTGATGCTAATAATG
upper sequence: GLYMA20G36180.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G098078_T01 (Zea mays), 3'ss of exon 4
-----------gtgagtgttcatgagctagatataaatatggtctttatggtcactagttgcttttttggtttttt-ctaacaaac-tttgcgtgttgcagGTTCATGGTAATGTTTGCTTGGCTAGTGTTGTTGTCACACAAACTTTGGACTGGAAACTCCATGCTTTTGATGTTCTATCAGAGTTTGAAGGGAGTAATG
||| | | | | || || |||| | | ||| | | ||| || || | | | | ||| | ||| | |||||||||| ||||| ||||| || ||||||||||| |||||||| |||| ||||| || ||||| || |||||||| ||||| ||||| | | ||||
aaatcaaaacagtggggtcttaacacataattagaaat-tacaaatgatgtaaatgatttgattcttaaatgatctgtttgcaatcacttgatcaatatagGTTCATGGGAATGTATGCTTAGCCAGTGTTGTTGTTACACAAACCCTGGATTGGAAGCTTCATGCCTTCGATGTTCTGTCAGAATTTGATGCTAACAATG
upper sequence: GLYMA20G36180.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G40730.1 (Arabidopsis thaliana), 3'ss of exon 4
----gtgagtgttcatga-gcta-gatataaatat---ggtcttta--tggtcactagttgcttttttggttttttctaacaaactttgc-gtgttg-cagGTTCATGGTAATGTTTGCTTGGCTAGTGTTGTTGTCACACAAACTTTGGACTGGAAACTCCATGCTTTTGATGTTCTATCAGAGTTTGAAGGGAGTAATG
|| |||| || | ||| || | ||| || | || ||| ||||| | |||||| ||| || || | | | || || ||||| ||||||||||| || |||| ||||||||||| |||| |||||||||||||||||||||||| |||||||||||||||||||||| ||||| ||||
gtaagtatctgtttataacactataattcagctattagagtatataaccggtggctagtcgattttttagttaaaactcttaagttctactgtcttaacagGTGCATGGTAATGTCTGTCTGGCAAGTGTTGTTGTTACACCTACTTTGGACTGGAAACTCCATGCTCTTGATGTTCTATCAGAGTTTGATGGGAGCAATG
upper sequence: GLYMA20G36180.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv13s0067g03110.t01 (Vitis vinifera), 3'ss of exon 4
------gtgagtgttcatgagctagatataaatatggtctttatgg---tcactagttgcttttttggtttt---ttctaacaaactttgcgtgttgcagGTTCATGGTAATGTTTGCTTGGCTAGTGTTGTTGTCACACAAACTTTGGACTGGAAACTCCATGCTTTTGATGTTCTATCAGAGTTTGAAGGGAGTAATG
|||| | | | | || | | | ||| | | || | | | || | | || |||| || | | ||| | | |||||||||||||||||||||||||| |||||||||||||| |||||| |||||||||| || ||||||||||| |||||||| |||||||| || || |
tgctcctctggtgtcacacaccacaaaacaagttagaaatctattggtgcctctgatatcatgttggatgttactttctgacgagcattggcttctacagGTTCATGGTAATGTTTGCTTGGCCAGTGTTGTTGTCACTCAAACTCTGGACTGGAAGCTGCATGCTTTTGACGTTCTATCTGAGTTTGATGGCCATAGCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttatggtcactagttgcttttttggttttttctaacaaactttgcgtgttgcagGTTCATGGTAATGTTTGCTTGGCTAGTGTTGTTGTCACACAAACTTTGGACTGGAAACTCCATGCTTTTGATGTTCTATCAGAGTTTGAAGGGAGTAATG
ttctaac putative branch site (score: 1)
ttttttggtttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtgttcatgagctagatataaatatggtctttatggtcactagttgcttttttggttttttctaacaaactttgcgtgttgcagGTTCATGGTAATGTTTGCTTGGCTAGTGTTGTTGTCACACAAACTTTGGACTGGAAACTCCATGCTTTTGATGTTCTATCAGAGTTTGAAGGGAGTAATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG