Sequence
atgc intronic sequence ATGC exonic sequence...atgttttaaaacattatgaggggctatccttttaaactatgatgttgagaaatatctgtttactagtgatcatctgactttactacgccttgtactgcagGAACATTTGTTAATAGTATGTGAACTACTTAAAGCCAACTTATATGAGTTTCACAAATTTAATCGAGAATCAGGGGGTGAAGTGTATTTCACGATGCCAA
Basic information
species | Glycine max |
transcript | GLYMA09G29970.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G29970.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G015073_T01 (Zea mays), 3'ss of exon 3
-atgttttaaaaca------ttatgaggggctatccttttaaactatgatgttgagaaatatctgtttactagtgatcatctgactttactacgccttgtactgcagGAACATTTGTTAATAGTATGTGAACTACTTAAAGCCAACTTATATGAGTTTCACAAATTTAATCGAGAATCAGGGGGTGAAGTGTATTTCACGATGCCAA
||| | | | | || | || | | | || | || | | | | || || | | || | | | ||| ||| |||||||||||||| | ||||| |||||||| || || || || | ||||||||||| ||||| || |||||||||||||||| || || ||||| |||||||
ggaatttcagagctcagggttgataattggttcttttccaaagcaatttgccttaaagtcacaacatttct--ttaccacttatttcaaatac----tgt-ttgcagGAACATTTGCTGATAGTCTGTGAACTTCTGAAGGCAAATCTGTATGAGTTTCAGAAATTCAACAGAGAATCAGGGGGTGAGGTTTACTTCACAATGCCAA
upper sequence: GLYMA09G29970.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G181002_T01 (Zea mays), 3'ss of exon 3
---atg-ttttaaaacattatgaggggctatccttttaaactatgatgttgagaaatatctgtttactagtgatcatctgactttactacgccttgtactgcagGAACATTTGTTAATAGTATGTGAACTACTTAAAGCCAACTTATATGAGTTTCACAAATTTAATCGAGAATCAGGGGGTGAAGTGTATTTCACGATGCCAA
||| | | || | | ||| || | | | || || | || | | | | | || | || | |||| | |||| ||||||| |||||| | ||||| |||||||| || || || || | || |||||||| ||||| || |||||||||||||||| || || ||||| |||||||
taaatgactcttctccaaaacaaattgctctcgagtcacagcatcatataataaagtttgttgtgtttgctgtactacttattttaa---acattgt-ttgcagGAGCATTTGCTGATAGTCTGTGAACTTCTGAAGGCAAATCTGTACGAGTTTCAGAAATTCAACAGAGAATCAGGGGGTGAGGTTTACTTCACAATGCCAA
upper sequence: GLYMA09G29970.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G73450.1 (Arabidopsis thaliana), 3'ss of exon 3
-------------------------------------------------------------------------------atgttttaaaacat-tatgaggggctatccttttaaactatgatgttgagaaatatctgtttactagtgatc--atctgac---tttactacgccttgtactgcagGAACATTTGTTAATAGTATGTGAACTACTTAAAGCCAACTTATATGAGTTTCACAAATTTAATCGAGAATCAGGGGGTGAAGTGTATTTCACGATGCCAA
||||| ||| | ||| ||||||| || ||| | || ||| ||| | | | | || || || || | ||||||| || ||| |||| ||||||||||| ||||| ||||| |||| ||||| ||||||||||| |||||||||| |||||||| ||||||||||||||||
gtaagtgattacatcccttttgcaaaatttggttttgctactgtatatcaaaagtgaccaattgtgtctttctcttcaacaattttagcacaagtgtgaaccatatgccttttatttaatacctttgcaatatttctctttgtggattgtttggtgtaacggattccctgaatgttct-ttgcagGAGCACTTGCTAATTGTATGTGAACTTCTTAAGGCCAATCTATACGAGTTCCACAAATTTAACAGAGAATCAGGTGGTGAAGTTTATTTCACGATGCCAA
upper sequence: GLYMA09G29970.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G17750.1 (Arabidopsis thaliana), 3'ss of exon 4
----------------------------------------------------------atgttttaaaac-attatg-aggggctatccttttaaactatgatgttgagaaata--tctgtttactagtg--atcatctgactttactacg---ccttgtactgcagGAACATTTGTTAATAGTATGTGAACTACTTAAAGCCAACTTATATGAGTTTCACAAATTTAATCGAGAATCAGGGGGTGAAGTGTATTTCACGATGCCAA
|| ||| | || ||| | | | | || | | || || || | || | | || || ||| ||| | | | || ||||||| || ||||||||||||||||||| || || || ||||| |||||||| || || |||||| | ||||||||||| || || |||||||| |||||||
gtaagtagatagatgcagaattgtatctttttcttttcaacaccgggtggatattctgctgctttggtgctatgatgtatcaattgttcgattcagtaaagaacatgggacgtgagcctacatcatgatgccattgactgtgattaattggaatctcagttttgcagGAGCACCTGTTAATAGTATGTGAACTTCTCAAGGCAAACTTGTATGAGTTCCAAAAGTTTAATAGGGAATCAGGGGGAGAGGTTTATTTCACTATGCCAA
upper sequence: GLYMA09G29970.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G73460.1 (Arabidopsis thaliana), 3'ss of exon 3
atgttttaaaacattatgaggggctatccttttaaactatgatgttgagaaatatc-tgtttactagtg-atcatctgactttact-acgccttgtac------tgcagGAACATTTGTTAATAGTATGTGAACTACTTAAAGCCAACTTATATGAGTTTCACAAATTTAATCGAGAATCAGGGGGTGAAGTGTATTTCACGATGCCAA
|| ||| || | | || || | ||||||| | | | | | ||| | | | | ||| || | || | || | || || | ||||||| || ||| |||| ||||||||||| ||||| ||||| |||| || || ||||||||||| |||||||||| |||||||| ||||||||||||||||
----attgaaatataaagggg-----tcataataaactaagtaggtttgcattattatatctctttgtggattgtttggtgtaacggattccctgaatgttctttgcagGAGCACTTGCTAATTGTATGTGAACTTCTTAAGGCCAATCTATACGAATTCCACAAATTTAACAGAGAATCAGGTGGTGAAGTTTATTTCACGATGCCAA
upper sequence: GLYMA09G29970.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv01s0011g01590.t01 (Vitis vinifera), 3'ss of exon 9
----atgttttaaaacattatgaggggctatccttttaaactatgatgttgagaaatatctgtttactagtgatcatctgactttactacgccttgtactgcagGAACATTTGTTAATAGTATGTGAACTACTTAAAGCCAACTTATATGAGTTTCACAAATTTAATCGAGAATCAGGGGGTGAAGTGTATTTCACGATGCCAA
|| | | | ||||| | | | | ||| || | | ||| | | | | ||| || |||||| | || | ||||||||||||| ||||| ||||| ||||| || || || ||||| ||||||||||| ||||||||| ||||||| || || || || || ||||| |||||||
gtttttgccatcatagtttatgcatttatggatgtctccaatatatgattttacagtgcctgctca--attagtcag--gagtttactttcctttattttgcagGAACATTTATTAATTGTATGCGAACTTCTCAAGGCAAACTTGTATGAGTTTCATAAATTTAATAGAGAATCCGGAGGGGAGGTTTACTTCACAATGCCAAMapped 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|151404434|gb|EV274248.1|EV274248EST: CTTCAGACAAGTACCACCTTCTAAGATTGTATGATTACTTCTATTATAGA GAACATTTGTTAATAGTATGTGAACTACTTAAAGCCAACTTATATGAGTTT
genomic: CTTCAGACAAGTACCACCTTCTAAGATTGTATGATTACTTCTATTATAGAgtaagtgaat ... tgtactgcagGAACATTTGTTAATAGTATGTGAACTACTTAAAGCCAACTTATATGAGTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgagaaatatctgtttactagtgatcatctgactttactacgccttgtactgcagGAACATTTGTTAATAGTATGTGAACTACTTAAAGCCAACTTATATGAGTTTCACAAATTTAATCGAGAATCAGGGGGTGAAGTGTATTTCACGATGCCAA
atctgac putative branch site (score: 3)
aatatct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgttttaaaacattatgaggggctatccttttaaactatgatgttgagaaatatctgtttactagtgatcatctgactttactacgccttgtactgcagGAACATTTGTTAATAGTATGTGAACTACTTAAAGCCAACTTATATGAGTTTCACAAATTTAATCGAGAATCAGGGGGTGAAGTGTATTTCACGATGCCAA
- - - -aaaacatt
- - - - - - - - tgagggg
- - - - - - - - - - - - - - - - - - - - gatgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctacgcc