Sequence
atgc intronic sequence ATGC exonic sequence...tttttttttcccagttaacaatagttttttataggtatctcctttttgtttcagtttttgctgttttgaccattgacataggagatgtttgtttcaccagGGAGCTGTTGGTTTGAGAATTAGAGTGTATGATCGGATAATGTGCTTTGTTAATTGTCACTTTGCTGCACATTTAGATGCAGTTGGTCGTCGCAACGCAG
Basic information
species | Glycine max |
transcript | GLYMA20G36090.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G36090.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G65580.1 (Arabidopsis thaliana), 3'ss of exon 5
-------------------------------------------------------------------------tttttttttcccagttaacaatagttttttataggtatctcctttttgtttcagtttttgctgttttgaccat----tgacataggagatgtttgtttcaccagGGAGCTGTTGGTTTGAGAATTAGAGTGTATGATCGGATAATGTGCTTTGTTAATTGTCACTTTGCTGCACATTTAGATGCAGTTGGTCGTCGCAACGCAG
|| | | || || || || |||| | | | || |||| || ||| | || | || ||| | || | |||| ||| |||| ||||| ||| || || | ||| |||||||||| || |||||||||| |||||||| |||||||||||| |||| || ||| ||| || || || |
gtatggtgccatattaggaaagttgctcacatttatcaacaataaaaagatctcataaaagggaaacaatggattatctcttaaca-ttgtcagatgtttgcttaaatggttcttttcccttttccattgttgtcatcttatctatattatgatagagccatttcttgtctcattagGGTGCTGTAGGTGTGCGACTCAGAATGTATGATCGAGTACTGTGCTTTGTAAATTGTCATTTTGCTGCACATCTAGAAGCTGTTAATCGGCGAAATGCTG
upper sequence: GLYMA20G36090.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv00s0220g00160.t01 (Vitis vinifera), 3'ss of exon 4
tttttttttcccagttaacaata-gttttttataggtatctcctttttgtttc-----agtttttgctgttttgaccattgacataggagatgtttgtttcaccagGGAGCTGTTGGTTTGAGAATTAGAGTGTATGATCGGATAATGTGCTTTGTTAATTGTCACTTTGCTGCACATTTAGATGCAGTTGGTCGTCGCAACGCAG
| || | | | || || |||| | | ||||||| | | ||||| | || | | |||||||||| | ||||| | | ||||||||||||||||||||||| ||||||||| ||||||||||||| ||||| || |||||||||||||| |||||||| ||||| |||||| || || |
------gcacttagaaagtggttcggttcataattgtattttccttttgttgcttgctatattttgttcttcttatgattgacatagctaaagtttggcttatcagGGAGCTGTTGGTTTGAGAATGAGAGTGTATAATCGGATAATGTGTTTTGTAAACTGTCACTTTGCTGCGCATTTAGAGGCAGTCAATCGTCGTAATGCGGMapped 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|7692411|gb|AW760518.1|AW760518EST: TCGAAGTGGCAGCAGTTCCATGTGGCTTTGGACGTGCTATTGGCAATAAG GGAGCTGTTGGTTTGAGAATTAGAGTGTATGATCGGATAATGTGCTTTGTT
genomic: TCGAAGTGGCAGCAGTTCCATGTGGCTTTGGACGTGCTATTGGCAATAAGgtgggcctgc ... gtttcaccagGGAGCTGTTGGTTTGAGAATTAGAGTGTATGATCGGATAATGTGCTTTGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtttcagtttttgctgttttgaccattgacataggagatgtttgtttcaccagGGAGCTGTTGGTTTGAGAATTAGAGTGTATGATCGGATAATGTGCTTTGTTAATTGTCACTTTGCTGCACATTTAGATGCAGTTGGTCGTCGCAACGCAG
cattgac putative branch site (score: 3)
tttgtttc putative PPT
agttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttttttttcccagttaacaatagttttttataggtatctcctttttgtttcagtttttgctgttttgaccattgacataggagatgtttgtttcaccagGGAGCTGTTGGTTTGAGAATTAGAGTGTATGATCGGATAATGTGCTTTGTTAATTGTCACTTTGCTGCACATTTAGATGCAGTTGGTCGTCGCAACGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - -ttcccag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgtt