Sequence
atgc intronic sequence ATGC exonic sequence...gttgtagttgctgacttgctgtttttggaaatgtttatgttttcacctcaactgttaatatgtaaaacttaaaaactgtatatttcacatttcattttagGTCTGGCGTATTAGGACTGGTCAGTGCTTGCGGCGTCTTGAACGTGCTCATTCTCAAGGTGTCACAAGTGTTTCCTTCTCTCGTGATGGAAGCCAGTTAT
Basic information
species | Glycine max |
transcript | GLYMA08G13560.2 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G13560.2 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G037683_T01 (Zea mays), 3'ss of exon 8
gttgtagttgctgacttgctgtttttggaaatgtttatgttttcacctca-actgttaatatgtaaaacttaaaaactgtatatttcacatttcattttagGTCTGGCGTATTAGGACTGGTCAGTGCTTGCGGCGTCTTGAACGTGCTCATTCTCAAGGTGTCACAAGTGTTTCCTTCTCTCGTGATGGAAGCCAGTTAT
||| | | | || | || | | | ||| | | | || |||| | | | || |||| | |||| |||||||| | ||||||||||||||||| || ||||| ||||| ||||| ||||||| ||||||||| | || || |||||||||| ||| |||
-ttggtaaactttatgcattattggtcagcatctgaacataatcatttgatgtaatctttacaattaactcctatgttaatattctcccattaattcccagGTTTGGCGTATACGAACTGGTCAGTGCTTGCGACGCCTTGAGCGTGCACATTCGAAAGGTGTTACAAGTGTTACATTTTCACGTGATGGAACCCAAATAT
upper sequence: GLYMA08G13560.2 (Glycine max), 3'ss of exon 9
lower sequence: AT1G73720.1 (Arabidopsis thaliana), 3'ss of exon 9
---------------------------------------------------------gttgtagttgctgacttgctgtttttggaaatgtttat-gttttcacctcaactgttaatatgta-aaacttaaaaactgtatattt-cacatttcatttt---agGTCTGGCGTATTAGGACTGGTCAGTGCTTGCGGCGTCTTGAACGTGCTCATTCTCAAGGTGTCACAAGTGTTTCCTTCTCTCGTGATGGAAGCCAGTTAT---
||| | | | | | | | | | | || | | || | | | | | | || ||| ||||||| | | ||| ||| ||| || |||||||||| ||||||||| ||| | || ||| |||| ||| ||||| ||||| || |||||| ||||||||||||| ||||||||||| |||
gtaagttccagctgcatatgtttccttaaagttgaattttttgtctgaagatagactattgcggcagtttggtagatatatcttcttcctctcattggtcccatatgtattctgattgaatacaaatagaaaaactagacttagatgcatgtcacttttgcagATCTGGCGTATAAGGACTGGTGTATGCATACGTCGTTTTGA---TGCACATTCCCAAGGAGTTACAAGTCTTTCCTTCTCTCGGGATGGAAGCCAATTACTGA
upper sequence: GLYMA08G13560.2 (Glycine max), 3'ss of exon 9
lower sequence: Vv17s0000g08930.t01 (Vitis vinifera), 3'ss of exon 9
gttgtagttgctgact-tgctgtttttggaaatgtttatgtttt-cacctcaactgttaatatg---taaaacttaaaaactgtatattt-cacatttcattt--tagGTCTGGCGTATTAGGACTGGTCAGTGCTTGCGGCGTCTTGAACGTGCTCATTCTCAAGGTGTCACAAGTGTTTCCTTCTCTCGTGATGGAAGCCAGTTAT
| | | | | ||||| || ||| || || || | | || || | | || | ||| || || | | ||||| || | | || | |||| |||||||| ||||||||||| ||||| || || ||||||||||| ||||| |||||||| |||||| || |||||||| |||||||| ||| ||
-------tctttcattatactgttggtg-aaacattggagtattgcttcaaaattggaagtttgacatcaaaattgaagatgatttatttgcaaactatatgtatcagGTGTGGCGTATAAGGACTGGTCAATGCTTACGCCGACTTGAACGTGCACATTCCCAAGGTGTTACAAGTCTTGTTTTCTCTCGAGATGGAAGTCAGATACMapped 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|193453833|gb|FK421170.1|FK421170EST: GCAGAGATTCAGAAATGCTTGCATCTGGGTCTCAAGATGGAAAGATTAAA GTCTGGCGTATTAGGACTGGTCAGTGCTTGCGGCGTCTTGAACGTGCTCAT
genomic: GCAGAGATTCAGAAATGCTTGCATCTGGGTCTCAAGATGGAAAGATTAAAgtgagtaata ... ttcattttagGTCTGGCGTATTAGGACTGGTCAGTGCTTGCGGCGTCTTGAACGTGCTCAT
EST:
gi|192300449|gb|FG987906.1|FG987906EST: GCAGAGATTCAGAAATGCTTGCATCTGGGTCTCAAGATGGAAAGATTAAA GTCTGGCGTATTAGGACTGGTCAGTGCTTGCGGCGTCTTGAACGTGCTCAT
genomic: GCAGAGATTCAGAAATGCTTGCATCTGGGTCTCAAGATGGAAAGATTAAAgtgagtaata ... ttcattttagGTCTGGCGTATTAGGACTGGTCAGTGCTTGCGGCGTCTTGAACGTGCTCAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctcaactgttaatatgtaaaacttaaaaactgtatatttcacatttcattttagGTCTGGCGTATTAGGACTGGTCAGTGCTTGCGGCGTCTTGAACGTGCTCATTCTCAAGGTGTCACAAGTGTTTCCTTCTCTCGTGATGGAAGCCAGTTAT
tgttaat putative branch site (score: 3)
tttcatttt putative PPT
ttaatatgtaaaactt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgtagttgctgacttgctgtttttggaaatgtttatgttttcacctcaactgttaatatgtaaaacttaaaaactgtatatttcacatttcattttagGTCTGGCGTATTAGGACTGGTCAGTGCTTGCGGCGTCTTGAACGTGCTCATTCTCAAGGTGTCACAAGTGTTTCCTTCTCTCGTGATGGAAGCCAGTTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG