Sequence
atgc intronic sequence ATGC exonic sequencegtaataattattttatgtgaatctgccctgcattagtttactgtattcaatctatgcctagacttaaaaatgcaatgcgttattttattttaaaaactaatgtgcttcacttttcctttctgttagGCATGGCAATATTTGATACAATGAGGCATATTCGACCTGATGTGTCCACTGTTTGCATTGGACTGGCAGCTAG
Basic information
species | Glycine max |
transcript | GLYMA03G37880.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G37880.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G121456_T03 (Zea mays), 3'ss of exon 5
gtaataattattttatgtgaatctgccctgcattagtttactgtattcaatctatgcctagacttaaaaatgcaatgcgttattttattttaaaaactaatgtgcttcacttttcctttctgttagGCATGGCAATATTTGATACAATGAGGCATATTCGACCTGATGTGTCCACTGTTTGCATTGGACTGGCAGCTAG
|| ||||| | ||| || ||| | | | || | || || ||||||| || ||| ||||||||||| ||||| |||||||||||||||| |||||| | |||||||| ||||||||||| |||||||| || || ||
---------------------------------------gtaatagctcatcta-acatag---tatgtctgcgtta-gctgcttcaatt--aatactaatg-----cattttcgttttctgttagGAATGGCTATATTTGATACAATGAAGCATATCAGGCCTGATGTATCCACTGTTTGTATTGGACTAGCTGCAAG
upper sequence: GLYMA03G37880.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G02560.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaataattattttatgtgaatctgccctgcattagtttactgtattca-atctatgcctagacttaaaaatgcaatgcgttattttattttaaaaactaatg--tgcttcacttttcctttctgttagGCATGGCAATATTTGATACAATGAGGCATATTCGACCTGATGTGTCCACTGTTTGCATTGGACTGGCAGCTAG
||| | | | || || | |||| | | || || ||| | ||||| | | || | | || ||||||||| ||||| ||||| |||||||| || || |||||||||||||||||||| |||| || || |||||
------------------------------------------gtaataacaactttgtc--agcttac---tctttatcttttttccggttttatggttaatgactcgtgcatctcttactttacccagGCATGGCTATATTCGATACTATGAGGCACATCCGGCCTGATGTGTCCACTGTTTGTGTTGGTCTAGCTGCTAG
upper sequence: GLYMA03G37880.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv07s0005g01530.t01 (Vitis vinifera), 3'ss of exon 5
gtaataattattttatg-tgaatctgccct-gcattagt-ttactgtattcaatctatgcctagacttaaaaatgcaatgcgttattttattttaaaaactaatgtgcttcacttttcctttctgttagGCATGGCAATATTTGATACAATGAGGCATATTCGACCTGATGTGTCCACTGTTTGCATTGGACTGGCAGCTAG
||||| | | ||| | ||| | | | || | || || | |||| || || | | | | | | | ||||||| || | |||| ||| | | | | ||||||||| ||||| || |||||||||||||| ||||||||||| |||||||| || ||||||| ||||| ||
gtaatttctgtcttacaataaatttttcttcacactggtactagtttatttaa-------ctgagcatggagacttg-tacaggttcttatttt-----cttgaattcttc-cttatttatcccctcagGCATGGCTATATTCGACACAATGAGGCATATCCGACCTGATGTTTCCACTGTGTGTGTTGGACTAGCAGCCAG
upper sequence: GLYMA03G37880.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S49_191V6.1 (Physcomitrella patens), 3'ss of exon 5
gtaataattattttatgtgaatctgccctgcattagtttac-tgtattcaatctatgcctagacttaaaaatgcaatgcgttattttattttaaaaactaatgtgcttcacttttcctttctgttagGCATGGCAATATTTGATACAATGAGGCATATTCGACCTGATGTGTCCACTGTTTGCATTGGACTGGCAGCTAG
|| || || | | || || | | ||| | | ||| | | | || ||| | ||||| | |||| | | ||| | ||| |||||||| || || || |||||||||||||||||||||||| ||| || || |||| || ||||| ||
--------------gtggacggtaattgtgagtttggtaacatgaagttcgtctggggtt---ctttaggttttatcttgtagtttcctcttaaagttt--tgtgtatgatttt--------gacagGAATGGCAATCTTCGACACCATGAGGCATATTCGACCTGATGTGAGCACAGTCTGTGTTGGGCTTGCAGCCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcaatgcgttattttattttaaaaactaatgtgcttcacttttcctttctgttagGCATGGCAATATTTGATACAATGAGGCATATTCGACCTGATGTGTCCACTGTTTGCATTGGACTGGCAGCTAG
aactaat putative branch site (score: 2)
tgcttcacttttcctt CT-rich tract
ttattttattttaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaataattattttatgtgaatctgccctgcattagtttactgtattcaatctatgcctagacttaaaaatgcaatgcgttattttattttaaaaactaatgtgcttcacttttcctttctgttagGCATGGCAATATTTGATACAATGAGGCATATTCGACCTGATGTGTCCACTGTTTGCATTGGACTGGCAGCTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT