Sequence
atgc intronic sequence ATGC exonic sequencegttagttagggaatctttcttagattgcttgctgtagcatatattatatgatcactgtggctgattttgaatttcttaatggacttgtagCAAATGTTTTTCACCGTGATCTAAAGCCAAAAAACATTTTAGCAAATGCTGACTGCAAACTGAAGATTTGTGACTTTGGTCTTGCCAGAGTGGCTTTCAA
Basic information
species | Glycine max |
transcript | GLYMA15G10940.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G10940.4 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os11g17080.1 (Oryza sativa), 3'ss of exon 2
----gttagttagggaatctttcttagattgcttgctgtagca---tatattatatgatcactgtggctgattttgaatttcttaatggactt---gtagCAAATGTTTTTCACCGTGATCTAAAGCCAAAAAACATTTTAGCAAATGCTGACTGCAAACTGAAGATTTGTGACTTTGGTCTTGCCAGAGTGGCTTTCAA
| | || | || | ||| | | || |||| || | | |||| || |||| | || || | ||||||||| |||||||| ||||| || |||||||| ||||| ||||||||||| || || || || || ||||| ||||| ||||| ||||| |||||||
agtagcctgatatgactgctccatctcattattcaatatattttgttatactagaattttactgatatgacagctgtctttcattatttgtttactgcagCAAATGTGTTTCACCGAGATCTTAAACCAAAAAATATTTTGGCAAATGCTGATTGTAAGCTCAAAATATGTGATTTTGGCCTTGCAAGAGTTGCTTTCAG
upper sequence: GLYMA15G10940.4 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G089484_T01 (Zea mays), 3'ss of exon 2
--gttagttagggaatctttcttagattgctt--gctgtagcatatattatatgatcactgtggctgattt------tgaatttcttaatggact--tgtagCAAATGTTTTTCACCGTGATCTAAAGCCAAAAAACATTTTAGCAAATGCTGACTGCAAACTGAAGATTTGTGACTTTGGTCTTGCCAGAGTGGCTTTCAA
||| ||||| || | | | || || ||||| | | | | | | | || ||||| | || || | | ||| | | || ||||||||| ||||| || ||||| || |||||||| ||| | ||||||||||| || || || || || ||||||||||| | || ||||| ||||||||
tcatta-ctaggggctcctaatctgtctgtttccgctgtgtccttt-tagtggcactaacatgcctgatatgactgatgcatctttcaatagcttattgcagCAAATGTATTTCATCGAGATCTCAAACCAAAAAATATTCTGGCAAATGCTGATTGTAAGCTCAAAATATGTGACTTTGGCTTAGCAAGAGTAGCTTTCAA
upper sequence: GLYMA15G10940.4 (Glycine max), 3'ss of exon 2
lower sequence: AT5G19010.1 (Arabidopsis thaliana), 3'ss of exon 2
gtta-gttagggaatctttcttagattgcttgctgtagcatatattatatgatca-ctgtggctgattttgaatttcttaatggacttgtagCAAATGTTTTTCACCGTGATCTAAAGCCAAAAAACATTTTAGCAAATGCTGACTGCAAACTGAAGATTTGTGACTTTGGTCTTGCCAGAGTGGCTTTCAA
|||| | ||| || | | ||| | | ||| ||| || |||||| | || | | | ||| || ||| ||| ||||| ||||| || ||||| || || |||||||| || ||||||||||| |||||||| ||||| ||||| ||||| ||||| ||||| || |||||
gttaagctagcgagcaat---aaaatttcattgattagtataagtt-tatgattatctttctgaaaatactttttttttctcttcctttcagCTAATGTCTTTCATCGGGATCTTAAACCCAAAAACATATTGGCAAATGCTGATTGCAAACTCAAGATCTGTGATTTTGGACTTGCAAGAGTCGCATTCAA
upper sequence: GLYMA15G10940.4 (Glycine max), 3'ss of exon 2
lower sequence: Vv05s0020g02530.t01 (Vitis vinifera), 3'ss of exon 2
---------------------------------------------------------------------------------------gttagttagggaatcttt--cttagattgcttgctgtagcatatattatatgatcactgtggctgattttgaatttcttaatggacttgtagCAAATGTTTTTCACCGTGATCTAAAGCCAAAAAACATTTTAGCAAATGCTGACTGCAAACTGAAGATTTGTGACTTTGGTCTTGCCAGAGTGGCTTTCAA
| ||| | | | | ||| | || ||| || | ||| ||| || | | || ||||| ||||||||||||| ||||| || ||||| || ||||| ||||| ||||||||||||||||||||||| ||||| ||||||||||||||||| ||||| || || ||
gttatatgatgctacaatattgtattttaactttttggccttggtttagcatactttattacaatctaattagcttgtgcagatggcatgagtaataatgtttataacttgaagtgggtgcccggatattcagtattccggtcctgattttgccat--atttctttaattcttttgtagCAAATGTCTTTCATCGGGATCTGAAACCAAAGAACATCTTAGCAAATGCTGACTGCAAACTCAAGATCTGTGACTTTGGTCTTGCAAGAGTAGCCTTTAA
upper sequence: GLYMA15G10940.4 (Glycine max), 3'ss of exon 2
lower sequence: PP1S80_71V6.2 (Physcomitrella patens), 3'ss of exon 2
--------gttagt-tagggaatctttcttagat-tgcttgctgtagcatatattatatgatcactgtggctgattttgaatttcttaatggacttgt--agCAAATGTTTTTCACCGTGATCTAAAGCCAAAAAACATTTTAGCAAATGCTGACTGCAAACTGAAGATTTGTGACTTTGGTCTTGCCAGAGTGGCTTTCAA
| | | || || | | ||| || | | | | || | | | || | ||||| || | | || | ||| |||| ||| ||||| ||||| || || || |||||||| ||| | || ||||| |||||||| |||||||| |||||||||||||| ||||| ||||||| || |
tcacaactctcactgtacaaaagactgatgggatgtggtcctttttggat-ttctgtctgttt-ttgtggatgttgacgtcttcatgtttgggattgttcagCTAATGTGTTTCATCGCGACCTGAAGCCAAAGAACGTGTTGGCAAACGCTGACTGTAAACTGAAAATTTGTGACTTTGGACTTGCTCGAGTGGCCTTTAGMapped 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|10238909|gb|BE807805.1|BE807805EST: CCAGTTTTTCTTGTATCAGCTTCTACGAGGCTTGAAGTATATACACACAG CAAATGTTTTTCACCGTGATCTAAAGCCAAAAAACATTTTAGCAAATGCTG
genomic: CCAGTTTTTCTTGTATCAGCTTCTACGAGGCTTGAAGTATATACACACAGgttagttagg ... ggacttgtagCAAATGTTTTTCACCGTGATCTAAAGCCAAAAAACATTTTAGCAAATGCTG
EST:
gi|193585418|gb|FK539097.1|FK539097EST: CCAGTTTTTCTTGTATCAGCTTCTACGAGGCTTGAAGTATATACACACAG CAAATGTTTTTCACCGTGATCTAAAGCCAAAAAACATTTTAGCAAATGCTG
genomic: CCAGTTTTTCTTGTATCAGCTTCTACGAGGCTTGAAGTATATACACACAGgttagttagg ... ggacttgtagCAAATGTTTTTCACCGTGATCTAAAGCCAAAAAACATTTTAGCAAATGCTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agcatatattatatgatcactgtggctgattttgaatttcttaatggacttgtagCAAATGTTTTTCACCGTGATCTAAAGCCAAAAAACATTTTAGCAAATGCTGACTGCAAACTGAAGATTTGTGACTTTGGTCTTGCCAGAGTGGCTTTCAA
tcttaat putative branch site (score: 3)
attttgaatttcttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagttagggaatctttcttagattgcttgctgtagcatatattatatgatcactgtggctgattttgaatttcttaatggacttgtagCAAATGTTTTTCACCGTGATCTAAAGCCAAAAAACATTTTAGCAAATGCTGACTGCAAACTGAAGATTTGTGACTTTGGTCTTGCCAGAGTGGCTTTCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA