Sequence
atgc intronic sequence ATGC exonic sequence...tataatatgacattggtaccatattattagcattgtgtttatttcataaatgtgcagttactggttgtggaagttaattgctgtaaatatttgtgtgcagGTGGTAGGAACTCCCAACTATATGTGTCCTGAACTTCTTGCAGATATTCCTTATGGATTCAAATCTGATATTTGGTCACTAG
Basic information
species | Glycine max |
transcript | GLYMA12G31330.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G31330.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv06s0009g00690.t01 (Vitis vinifera), 3'ss of exon 8
--tataatatgacattggtaccatattattagcattgtgtttatttcataaatgtgcagttactggttgtgga-agttaattgctgtaaatatttgtgtgcagGTGGTAGGAACTCCCAACTATATGTGTCCTGAACTTCTTGCAGATATTCCTTATGGATTCAAATCTGATATTTGGTCACTAG
| ||| | | || | | || ||| | || ||||| || || | || | | || | | | | |||| ||||| || ||||||||||| || ||||||||||||||||||||||||||||||||||| |||||||||||||| ||||| ||||
gttgaaatcttgc-ctgtgcttgtcctgttgatatt-cacggacttggtaaatttg-agcaatgggacacgctcacctattcatttcctacttatgtgcacagGTAGTTGGAACTCCCAATTACATGTGTCCTGAACTTCTTGCAGATATTCCTTATGGCTTCAAATCTGATATCTGGTCTCTAG
upper sequence: GLYMA12G31330.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S22_216V6.1 (Physcomitrella patens), 3'ss of exon 8
---------------------------------------------------tataatatgacattggtaccatattattagcattgtgtttatttcataaatgtgcagttactggttgtggaagttaattgctgtaaatatttgtgtgcagGTGGTAGGAACTCCCAACTATATGTGTCCTGAACTTCTTGCAGATATTCCTTATGGATTCAAATCTGATATTTGGTCACTAG
| | || |||||| | | | |||| ||| | | || | | | ||| | | ||||| | | | ||||||| ||||| ||||| || || |||||||| || || |||||||| || || |||||||||||||| || ||||||||| |||
gtaagtaatccgttgtgaacctcgtatcatttgcattggaatgatgatcgctgctgtgaatagtttttaccatctcgcggtcgtactgttcgtttggaagttaatcaat--ccactaatggccggaacgtgctgcttcttgctat-tgcagGTAGTAGGCACTCCAAATTACATGTGTCCAGAGCTACTTGCAGACATCCCATATGGATTCAAATCAGACATTTGGTCATTAG
upper sequence: GLYMA12G31330.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ32716 (Selaginella moellendorffii), 3'ss of exon 8
tataatatgacattggtaccatattattagcattgtgtttatttcataaatgtgcagttactggttgtggaagttaatt--gctgtaaatatttgtgtgcagGTGGTAGGAACTCCCAACTATATGTGTCCTGAACTTCTTGCAGATATTCCTTATGGATTCAAATCTGATATTTGGTCACTAG
| | | ||| ||| || |||| | | || | | |||||||||| || || || || |||||||| || ||||||||||| || || || ||||| |||||||| ||||| ||||| |||
-------------------------------------------------gtaagttctattctgttttggcagcgaatttgacaggaagaaaacat-tgcagGTGGTTGGGACCCCAAATTATATGTGCCCGGAACTTCTTGCCGACATCCCATATGGCTTCAAATCAGATATATGGTCGTTAG
upper sequence: GLYMA12G31330.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ20709 (Selaginella moellendorffii), 3'ss of exon 8
tataatatgacattggtaccatattattagcattgtgtttatttcataaatgtgcagttactggttgtggaagttaattgctgtaaatatttgtgtgcagGTGGTAGGAACTCCCAACTATATGTGTCCTGAACTTCTTGCAGATATTCCTTATGGATTCAAATCTGATATTTGGTCACTAG
||| | | | ||||| || | | ||| || | |||||||||| || || || || |||||||| || ||||||||||| || || || ||||| |||||||| ||||| ||||| |||
---------------------------------------------gtaagt-tcta--tactgttttctcagccaatttgacaggaagaaaacattgcagGTGGTTGGGACCCCAAATTATATGTGCCCGGAACTTCTTGCCGACATCCCATATGGCTTCAAATCAGATATATGGTCGTTAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataaatgtgcagttactggttgtggaagttaattgctgtaaatatttgtgtgcagGTGGTAGGAACTCCCAACTATATGTGTCCTGAACTTCTTGCAGATATTCCTTATGGATTCAAATCTGATATTTGGTCACTAG
agttaat putative branch site (score: 4)
tgtaaatattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tataatatgacattggtaccatattattagcattgtgtttatttcataaatgtgcagttactggttgtggaagttaattgctgtaaatatttgtgtgcagGTGGTAGGAACTCCCAACTATATGTGTCCTGAACTTCTTGCAGATATTCCTTATGGATTCAAATCTGATATTTGGTCACTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - tgcagtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgta