Sequence
atgc intronic sequence ATGC exonic sequence...tgaacactagaattagaaaagggaaaatggcctaggtcttataatttttttccccatcataactattgtgttgctgtaattcttcatggttttgtatcagATATGTGCTGAACTCACCTCGTATGAAGAAGTTTTTTGACTATATCCAACTTCCAAATTTTGACATTGCTGCGGATGCTGCAGCAACCTTTAAG
Basic information
species | Glycine max |
transcript | GLYMA15G12220.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G12220.2 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os07g39630.1 (Oryza sativa), 3'ss of exon 4
----tgaacactagaatt---agaaaagggaaaatggcctaggtcttataatttttttccccatcataactattgtgttgctgtaattcttcatggttttgtatcagATATGTGCTGAACTCACCTCGTATGAAGAAGTTTTTTGACTATATCCAACTTCCAAATTTTGACATTGCTGCGGATGCTGCAGCAACCTTTAAG
| | | | || | ||| ||||| ||| ||| || || | | | || | | | |||| | |||| | ||| || || | | || | ||||||||||| ||||||||||| ||||||||||||||||||||||| | |||||| | || |||||||||
caactaaggattctgttttacataaaccataaaatactgtagaaattagaaattcctgtcggaatggtgcttatttatcttggtaaatgttcac-------tcacagGTACGTTTTAGAGTCTGACCACATGAAGAAGTTCTTTGACTATATACAACTTCCAAATTTTGACATTGCATCAGATGCTTCTGCGACCTTTAAG
upper sequence: GLYMA15G12220.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G066051_T01 (Zea mays), 3'ss of exon 4
---tgaaca-ctagaattagaaaagggaaaatggcc-taggtcttataatttttttccccatcataactattgtgttgctgtaattcttcatggttttgtatcagATATGTGCTGAACTCACCTCGTATGAAGAAGTTTTTTGACTATATCCAACTTCCAAATTTTGACATTGCTGCGGATGCTGCAGCAACCTTTAAG
| ||| | | || || | ||||| | || || || | | | | | | | || | || ||| ||| | ||| ||||| | | || | ||||||||||| ||||||||||| || ||||||||||||||||| ||| | |||||| | || |||||||||
agctagacatccatgatccataagtgcaaaatttttgttggagttggaagctcctgtggacttttgg-tgctattttcttatagaactt----gttcattgacagGTATGTTTTAGAGTCTGAACACATGAAGAAGTTCTTTGACTATATACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCGGCTACCTTTAAG
upper sequence: GLYMA15G12220.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G351417_T02 (Zea mays), 3'ss of exon 3
tgaacactagaattagaaaagggaaaatggcctaggtcttat--aatttttttccccatcataactattg-tgttgctgtaattcttcatggttttgt-atcagATATGTGCTGAACTCACCTCGTATGAAGAAGTTTTTTGACTATATCCAACTTCCAAATTTTGACATTGCTGCGGATGCTGCAGCAACCTTTAAG
| |||| | || || | || || | | | || | || | | ||| ||| ||| || | | | | ||| || | ||| ||||| | | || | |||||||||||| || |||||||| || ||||||||||||||||| ||| | |||||| | || |||||||||
--attacta-agttggacatccataagtg-caaaaatattgtcgaaactagaggctcatgtggacttttggtgctattttcttatagaatgtcttcattgacagGTATGTTTTAGAGTCCGAACATATGAAGAAGTTCTTCGACTATATACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCTGCTACCTTTAAG
upper sequence: GLYMA15G12220.2 (Glycine max), 3'ss of exon 2
lower sequence: AT5G47540.1 (Arabidopsis thaliana), 3'ss of exon 4
-tgaac-actagaattagaaaagggaaa--atggcctaggtcttataatttttttccccatcataactattgtgttgctgtaattcttcatggttttgtat-cagATATGTGCTGAACTCACCTCGTATGAAGAAGTTTTTTGACTATATCCAACTTCCAAATTTTGACATTGCTGCGGATGCTGCAGCAACCTTTAAG
||| | | | | | | | | | |||| | || | | | | | | ||||| || | ||| || |||| || ||||||||| || | || | | ||||||| || ||||| || || || ||||||||||| ||||||||||| |||||||| || || ||||||
gtgagccaatcgtttcattttcttcattttacgacctatggagta-attatggattcagagaataacggaaaatgtgtttactaacttaatttctttggattcagATATGTTTTGGAGTCTGACCATGTGAAGAAATTCTTTGATTACATACAGCTTCCAAATTTCGACATTGCTGCCGATGCTGCTGCTACTTTTAAG
upper sequence: GLYMA15G12220.2 (Glycine max), 3'ss of exon 2
lower sequence: AT4G17270.1 (Arabidopsis thaliana), 3'ss of exon 4
----------tgaacactagaattagaaaagggaaaatggcctaggtcttataatttttttccccatcataactattgtgttgctgtaatt----cttcatggttttgtat----cagATATGTGCTGAACTCACCTCGTATGAAGAAGTTTTTTGACTATATCCAACTTCCAAATTTTGACATTGCTGCGGATGCTGCAGCAACCTTTAAG
| | | || | | || | |||| | || ||| | | || |||| | || | || | || | | ||| ||| ||||||||| || |||| | |||||||||||||| |||| || || ||||| ||||| ||||||||||| |||||||| ||||| ||||||
gtgagcaaatcttatattttctttgattacgagattaaatcctatatgtttcaatccataaagagacaatctctatcgaatttatatagtgaaaactgcttctctttctatggttcagATATGTTTTGGACTCGGAGCACGTGAAGAAGTTTTTTTACTACATACAGCTTCCCAATTTCGACATTGCTGCTGATGCTGCTGCAACTTTTAAG
upper sequence: GLYMA15G12220.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv10s0405g00020.t01 (Vitis vinifera), 3'ss of exon 4
tgaacactagaattagaaaagggaaaatggcc-taggtcttataatttttttccccatcataactattgtgttgctgtaattcttc------atggttttgtatc----agATATGTGCTGAACTCACCTCGTATGAAGAAGTTTTTTGACTATATCCAACTTCCAAATTTTGACATTGCTGCGGATGCTGCAGCAACCTTTAAG
| ||||| | || | || | |||| ||| || | || ||| || || | | | ||| |||||||| | | || || || ||| | ||| | | ||||||||||||||||| ||||| |||||||||||||||||||||||||| |||||||| ||||| ||||||
-----------ctgtccaaaggcagtttgacaatatcttttattattattattattattatatgggtttaactgagttgaattttctaatttatggtttttttcctgacagGTACGTCCTGGAATCAGCGCACATGAAGAAGTTTTTTGATTATATTCAACTTCCAAATTTTGACATTGCTGCAGATGCTGCTGCAACTTTTAAGMapped 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|10231690|gb|BE800578.1|BE800578EST: CACTATGGTGCGATGCTGAGGGAGTGCATAAGACACCAGATTGTTGCAAA ATATGTGCTGAACTCACCTCGTATGAAGAA
genomic: CACTATGGTGCGATGCTGAGGGAGTGCATAAGACACCAGATTGTTGCAAAgtaaggaaaa ... tttgtatcagATATGTGCTGAACTCACCTCGTATGAAGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttttccccatcataactattgtgttgctgtaattcttcatggttttgtatcagATATGTGCTGAACTCACCTCGTATGAAGAAGTTTTTTGACTATATCCAACTTCCAAATTTTGACATTGCTGCGGATGCTGCAGCAACCTTTAAG
tcataac putative branch site (score: 2)
ataactatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgaacactagaattagaaaagggaaaatggcctaggtcttataatttttttccccatcataactattgtgttgctgtaattcttcatggttttgtatcagATATGTGCTGAACTCACCTCGTATGAAGAAGTTTTTTGACTATATCCAACTTCCAAATTTTGACATTGCTGCGGATGCTGCAGCAACCTTTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttcatgg