Sequence
atgc intronic sequence ATGC exonic sequencegtaacatagtatttttactctgtagtacaaaatctttaatataacaatcaagtgctaactcaaaattcatactgcacagGTTGGTCTACTGAATGTTGACGGTTACTATAACTGTTTGCTTGCATTATTTGACAATGGTGTTAAAGAAGGTTTCATTAAGCCTTGTGCACGGAATATAG
Basic information
species | Glycine max |
transcript | GLYMA04G05550.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G05550.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G11950.1 (Arabidopsis thaliana), 3'ss of exon 5
------gtaacatagtatttttactctgtagtacaaaatctttaatataacaatcaagtgctaactcaaaattcatactgcacagGTTGGTCTACTGAATGTTGACGGTTACTATAACTGTTTGCTTGCATTATTTGACAATGGTGTTAAAGAAGGTTTCATTAAGCCTTGTGCACGGAATATAG
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gtatttttaacat--ttcctttgctcagtcaaagaagtatgctactaattcctctgttgattagtttgggattgtttctgt--agGTTGGTCTATTGAATGTTGATGGGTACTATAACAATTTGCTTGCTTTATTTGATACCGGTGTCGAAGAAGGTTTTATCAAGCCAGGTGCACGTAACATTG
upper sequence: GLYMA04G05550.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G26140.1 (Arabidopsis thaliana), 3'ss of exon 3
----gtaacatagtat-ttttactc---tgta---gtacaaaatctttaatataacaatcaagtgctaactcaaaatt----catactgcacagGTTGGTCTACTGAATGTTGACGGTTACTATAACTGTTTGCTTGCATTATTTGACAATGGTGTTAAAGAAGGTTTCATTAAGCCTTGTGCACGGAATATAG
| ||| || ||||||| |||| || || | | ||| | | | || | | || || || | ||||||||||| |||||||||| |||||||||||| ||||||||| || ||||||| ||| ||| |||||||||| ||||| | |||| | ||||| |
gtagttgacaccgttccttttactggtatgtatctatataagaagatagata-gatactatgttgatgatgagaatttggattattttctgcagGTTGGTCTTTTGAATGTTGATGGTTACTATAACAATTTGCTTGCTTTCTTTGACACTGGAGTTGAAGAAGGTTTTATTAAACAAGGTGCTTGTAATATCG
upper sequence: GLYMA04G05550.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv04s0008g01040.t01 (Vitis vinifera), 3'ss of exon 5
-------------------------gtaacatagtatttttactctgtagtacaaaatctttaatataacaatcaagtgctaactcaaaattcatactgcacagGTTGGTCTACTGAATGTTGACGGTTACTATAACTGTTTGCTTGCATTATTTGACAATGGTGTTAAAGAAGGTTTCATTAAGCCTTGTGCACGGAATATAG
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tatagatcaaaaatgcaaaatcctgttagagtggcaatttcatgagagaatattggatg---aggtgaacaataatatcttaattaggcatt-actctacacagGTTGGTCTGCTAAATGTTGATGGGTACTACAACTTTTTGCTTGCATTATTTGACAACGGTGTCAAAGAAGGCTTCATCAAGCCAGGTGCTCGGCATATAGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|209721045|gb|BW666302.1|BW666302EST: AGCTGTTGGAGATGATAACTTGGGCCCAACTTGGAATCCATAAAAAACCG GTTGGTCTACTGAATGTTGACGGTTACTATAACTGTTTGCTTGCATTATTT
genomic: AGCTGTTGGAGATGATAACTTGGGCCCAACTTGGAATCCATAAAAAACCGgtaacatagt ... tactgcacagGTTGGTCTACTGAATGTTGACGGTTACTATAACTGTTTGCTTGCATTATTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtacaaaatctttaatataacaatcaagtgctaactcaaaattcatactgcacagGTTGGTCTACTGAATGTTGACGGTTACTATAACTGTTTGCTTGCATTATTTGACAATGGTGTTAAAGAAGGTTTCATTAAGCCTTGTGCACGGAATATAG
tgctaac putative branch site (score: 1)
aaatctttaatataac 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacatagtatttttactctgtagtacaaaatctttaatataacaatcaagtgctaactcaaaattcatactgcacagGTTGGTCTACTGAATGTTGACGGTTACTATAACTGTTTGCTTGCATTATTTGACAATGGTGTTAAAGAAGGTTTCATTAAGCCTTGTGCACGGAATATAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG