Sequence
atgc intronic sequence ATGC exonic sequence...tgatcatcttgttctccatatcatgcctttgcacttgatacattattatttggcacccaatcatcataacgatttacattttcattttctctacatatagCTTTTATGCTGCGGAGGTCCTGCTTGCTCTTGAGTATCTTCACATGCTTGGAGTTGTGTATAGAGACCTCAAACCTGAAAATGTGTTGGTCCGAGATGAT
Basic information
species | Glycine max |
transcript | GLYMA07G13960.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G13960.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv15s0021g01540.t01 (Vitis vinifera), 3'ss of exon 2
-tgatcatcttgttctccatatcatgcc-tttgcacttgatacatt--attatttggcacccaatcatcataacgatttacattttcattttctctacatatagCTTTTATGCTGCGGAGGTCCTGCTTGCTCTTGAGTATCTTCACATGCTTGGAGTTGTGTATAGAGACCTCAAACCTGAAAATGTGTTGGTCCGAGATGAT
| | || | |||| | ||| || | | |||| || ||| || ||| ||| ||| | ||| | | | | | | || ||||||||||| ||||| || | || ||||||||||| ||||||||||||||||| || | || | ||||| |||||||| || ||||| ||||||
tcccactttttaaaaccttagtcatactgttttcaactttttcatttcgttgtttttcaagcaaa-gcagtaatgatcaatgtttatactat---tgcctgcagGTTTTATGCTGCAGAGGTTCTATTAGCACTTGAGTATCTCCACATGCTTGGAGTTGTCTACCGGGATTTGAAACCAGAAAATGTTTTAGTCCGTGATGATMapped 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|12773484|gb|BG238411.1|BG238411EST: ACTTTACGGCAGCGACAACCTGGGAAACATTTCTCAGAATATGCTGCACG CTTTTATGCTGCGGAGGTCCTGCTTGCTCTTGAGTATCTTCACATGCTTGG
genomic: ACTTTACGGCAGCGACAACCTGGGAAACATTTCTCAGAATATGCTGCACGgtatgctgta ... ctacatatagCTTTTATGCTGCGGAGGTCCTGCTTGCTCTTGAGTATCTTCACATGCTTGG
EST:
gi|9259113|gb|BE347260.1|BE347260EST: ACTTTACGGCAGCGACAACCTGGGAAACATTTCTCAGAATATGCTGCACG CTTTTATGCTGCGGAGGTCCTGCTTGCTCTTGAGTATCTTCACATGCTTGG
genomic: ACTTTACGGCAGCGACAACCTGGGAAACATTTCTCAGAATATGCTGCACGgtatgctgta ... ctacatatagCTTTTATGCTGCGGAGGTCCTGCTTGCTCTTGAGTATCTTCACATGCTTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatttggcacccaatcatcataacgatttacattttcattttctctacatatagCTTTTATGCTGCGGAGGTCCTGCTTGCTCTTGAGTATCTTCACATGCTTGGAGTTGTGTATAGAGACCTCAAACCTGAAAATGTGTTGGTCCGAGATGAT
tcataac putative branch site (score: 2)
cattttcattttctct putative PPT
atttacattttcattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgatcatcttgttctccatatcatgcctttgcacttgatacattattatttggcacccaatcatcataacgatttacattttcattttctctacatatagCTTTTATGCTGCGGAGGTCCTGCTTGCTCTTGAGTATCTTCACATGCTTGGAGTTGTGTATAGAGACCTCAAACCTGAAAATGTGTTGGTCCGAGATGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - -ttctcca
- - - - - - - - - - -catgcct
- - - - - - - - - - - - - - -tgcactt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ccaatca