Sequence
atgc intronic sequence ATGC exonic sequence...atttgtttttcgtagtatggagtgaatgatttcaagatgttatgattattaggttaactacacatgttatctttgctgacatccttatttttgtctgcagGCAATGTATAATGAGTTCTCAACAGCCAACATACAGATTGACAAAGATTTCAGTGCAAAGCTTTCAGGATATGGTTGTGTTGGACATATTCCCGAGGAAG
Basic information
species | Glycine max |
transcript | GLYMA09G41160.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G41160.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g60700.2 (Oryza sativa), 3'ss of exon 3
-----------------atttgtttttcgtagtatg---gagtgaatg---atttcaagatgttatg-attat-taggttaactacacatgttatctttgctgacatccttatt----------tttgtctgcagGCAATGTATAATGAGTTCTCAACAGCCAACATACAGATTGACAAAGATTTCAGTGCAAAGCTTTCAGGATATGGTTGTGTTGGACATATTCCCGAGGAAG
||| ||||| | || ||||||| |||| | ||||| | || | |||| | || | | | | | | |||||| ||| | | ||||| ||||| ||||| |||||||| | ||||| || |||||||||||||||| ||||||||| ||||||||||| ||||||||| | | ||||||| |
gttactgcttctaaactttttctttttgacattaccaataagtgaatatttattttacctagttatatagtacattggttgatggtttttgaccttgtggtttaaactcttattcatatgttattttttttacagGCCATGTACAATGACTTCTCAACCTCAAACATCCAAATTGACAAAGATTTCACTGCAAAGCTATCAGGATATGGATGTGTTGGATTCAATACCGAGGAGG
upper sequence: GLYMA09G41160.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G143790_T01 (Zea mays), 3'ss of exon 1
----------------------atttgtttttcgtagtatggagtgaatgatttcaagatgttatg----att-------attaggtta-actac--acatgttatctttgctgacatccttatttttgtctg-----cagGCAATGTATAATGAGTTCTCAACAGCCAACATACAGATTGACAAAGATTTCAGTGCAAAGCTTTCAGGATATGGTTGTGTTGGACATATTCCCGAGGAAG
| | | | | | | | || ||| || | |||| ||| |||| ||| | ||| | | | ||| || || ||||| | || ||||| ||||| || ||||||||||| ||||| || || || |||| ||||| ||| |||||||||||||||||||||||||| | | |||||||
gtgagcatgctacttgatttatggtcttatggcatcacacaaaaggtgtgcttttaattttttatttggcattcaaccacattatcttataataccgagccgctgacttaacttgtatttatatttccatttgtttttcagGCCATGTACAACGAGTTCTCAACTTTGAACATCCAAATAGATAAAGGTTTCACTGCTAAGCTTTCAGGATATGGTTGTGTTGGCTTCAATACCGAGGAGA
upper sequence: GLYMA09G41160.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM5G828466_T01 (Zea mays), 3'ss of exon 1
-------------------------------------------atttgtttttcgtagtatggagtgaatgatttcaagatgttatgattattaggtt-aactacacatgttatctttgctgacatccttatttttgtctgcagGCAATGTATAATGAGTTCTCAACAGCCAACATACAGATTGACAAAGATTTCAGTGCAAAGCTTTCAGGATATGGTTGTGTTGGACATATTCCCGAGGAAG
| ||| || | | | | | ||| | | |||| |||| | | | || | | | | | | | || |||| | | | ||||| | ||| || ||||||||||| ||||| || || || |||| ||||| ||| |||||||||||||||||||||||||| | | |||||||
gtgagcatgctacttgatttatggtcttatggcatcacataaaaggtgtgcttttaattttttatttggc-attcaaccacattatc-ttataataccgagccactgacttaacttgtatttatatttccatttgttttt-cagGCCACGTACAACGAGTTCTCAACTTTGAACATCCAAATAGATAAAGGTTTCACTGCTAAGCTTTCAGGATATGGTTGTGTTGGCTTCAATACCGAGGAGA
upper sequence: GLYMA09G41160.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G010453_T01 (Zea mays), 3'ss of exon 1
-------------------------------------------atttgtttttcgtagtatggagtgaatgatttcaagatgttatgattattaggtt-aactacacatgttatctttgctgacatccttatttttgtctgcagGCAATGTATAATGAGTTCTCAACAGCCAACATACAGATTGACAAAGATTTCAGTGCAAAGCTTTCAGGATATGGTTGTGTTGGACATATTCCCGAGGAAG
| ||| || | | | | | ||| | | |||| |||| | | | || | | | | | | | || |||| | | | ||||| | ||| || ||||||||||| ||||| || || || |||| ||||| ||| |||||||||||||||||||||||||| | | |||||||
gtgagcatgctacttgatttatggtcttatggcatcacataaaaggtgtgcttttaattttttatttggc-attcaaccacattatc-ttataataccgagccactgacttaacttgtatttatatttccatttgttttt-cagGCTACGTACAACGAGTTCTCAACTTTGAACATCCAAATAGATAAAGGTTTCACTGCTAAGCTTTCAGGATATGGTTGTGTTGGCTTCAATACCGAGGAGA
upper sequence: GLYMA09G41160.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G068151_T01 (Zea mays), 3'ss of exon 3
-----------atttg-tttttcgtagtatggagtgaatgatttca-agatgttatgattattaggtt-aactacacatgttatctttgctgacatccttatttttgtctgcagGCAATGTATAATGAGTTCTCAACAGCCAACATACAGATTGACAAAGATTTCAGTGCAAAGCTTTCAGGATATGGTTGTGTTGGACATATTCCCGAGGAAG
| ||| ||| | || ||||| | || || | | | | || || | | | | | | | | | | | | || |||| | | | ||||| ||||| | ||||||||||| ||||| || || || |||| ||||| ||| |||||||||||||||||||||||||| | | |||||||
gtgatcatgctacttgatttatggtcttatgggctatggcatcacacaaaaggtgtgcttttaataccgagccgctgacttaacttgtatttatatttccatttgttttt-cagGCCATGTACAGCGAGTTCTCAACTTTGAACATCCAAATAGATAAAGGTTTCACTGCTAAGCTTTCAGGATATGGTTGTGTTGGCTTCAATACCGAGGAGA
upper sequence: GLYMA09G41160.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G079117_T01 (Zea mays), 3'ss of exon 1
---------------------------------------------atttgtttttcgtagtatggagtgaatgatttcaagatgttatgattattaggtt-aactacacatgttatctttgctgacatccttatttttgtctgcagGCAATGTATAATGAGTTCTCAACAGCCAACATACAGATTGACAAAGATTTCAGTGCAAAGCTTTCAGGATATGGTTGTGTTGGACATATTCCCGAGGAAG
| || |||| | | | | | ||| | | |||| |||| | | | | | | | | | | | || |||| || | ||||| || || || ||||||||||| ||||| || || || |||| ||||| ||| |||||||||||||||||||||||||| | | |||||||
gtgagcatgctacttgatttatggtcttatggcatcacacaaaaggtgtgcttttaattttttttatttggc-attcaaccacattatc-ttataataccgagccgctgacttaacttgtatttatatttccatttg-gttttcagGCCATATACAACGAGTTCTCAACTTTGAACATCCAAATAGATAAAGGTTTCACTGCTAAGCTTTCAGGATATGGTTGTGTTGGCTTCAATACCGAGGAGA
upper sequence: GLYMA09G41160.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G380227_T02 (Zea mays), 3'ss of exon 2
---------------------------------------------------------atttgtttttcgtagtatggagtgaatgatttcaagatgttat---------gattattaggt-taactacaca----tgttatctttgctgacatccttatttttgtctg-----cagGCAATGTATAATGAGTTCTCAACAGCCAACATACAGATTGACAAAGATTTCAGTGCAAAGCTTTCAGGATATGGTTGTGTTGGACATATTCCCGAGGAAG-
| | | | | | | | || ||| || | |||| | | | | | | | || || | ||| ||| || ||||| | || ||||| ||||| || ||||||||||| ||||| || || || |||| ||||| ||| |||||||||||||||||||||||||| | | |||||||
gtctagctttcttgcatgatgaaggaccctttcaggtgagcatgctacttgatttatggtcttatggcatcacacaaaaggtgtgcttttaattttttatttggcattcaaccacaatatcttataataccgagctgctgacttaactggtatttatatttccatttgtttttcagGCCATGTACAACGAGTTCTCAACT-TGAACATCCAAATAGATAAAGGTTTCACTGCTAAGCTTTCAGGATATGGTTGTGTTGGCTTCAATACCGAGGAGAT
upper sequence: GLYMA09G41160.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G380227_T01 (Zea mays), 3'ss of exon 2
----------------------atttgtttttcgtagtatggagtgaatgatttcaagatgttat---------gattattaggt-taactacaca----tgttatctttgctgacatccttatttttgtctg-----cagGCAATGTATAATGAGTTCTCAACAGCCAACATACAGATTGACAAAGATTTCAGTGCAAAGCTTTCAGGATATGGTTGTGTTGGACATATTCCCGAGGAAG-
| | | | | | | | || ||| || | |||| | | | | | | | || || | ||| ||| || ||||| | || ||||| ||||| || ||||||||||| ||||| || || || |||| ||||| ||| |||||||||||||||||||||||||| | | |||||||
gtgagcatgctacttgatttatggtcttatggcatcacacaaaaggtgtgcttttaattttttatttggcattcaaccacaatatcttataataccgagctgctgacttaactggtatttatatttccatttgtttttcagGCCATGTACAACGAGTTCTCAACT-TGAACATCCAAATAGATAAAGGTTTCACTGCTAAGCTTTCAGGATATGGTTGTGTTGGCTTCAATACCGAGGAGAT
upper sequence: GLYMA09G41160.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv08s0058g01290.t01 (Vitis vinifera), 3'ss of exon 3
atttgtttttcgtagtatggagtgaatg----atttcaagatgttatgattattaggttaactacacatgttatctttgctgacatccttatttt-tgtctgcagGCAATGTATAATGAGTTCTCAACAGCCAACATACAGATTGACAAAGATTTCAGTGCAAAGCTTTCAGGATATGGTTGTGTTGGACATATTCCCGAGGAAG
| | || | | | ||| || | | ||| || | || | | | | |||| | | |||| | | | | | ||| | ||||| ||||| ||||| || ||||| ||||| |||||||||||||| ||||| |||||||||||||| ||||||||||| ||||| || ||||| || | ||
---tttccctcagatcactgtcccaattctgtatattaggattttttttttccagtggttgttgttcttgttgtg--tactgagaacttccctgtgtgtttacagGCTATGTACAATGAATTTTCAACTGCCAATATACAGATTGACAAGGATTTTAGTGCAAAGCTTTCGGGATATGGTTGCGTTGGCCACATTCCAGAAGCAGMapped 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|15203966|gb|BI426743.1|BI426743EST: TATGTGCTGCACAAGGTCTAACTTTCTTGCATGAAGAAGGGCCTTTTCAG GCAATGTATAATGAGTTCTCAACAGCCAACATACAGATTGACAAAGATTTC
genomic: TATGTGCTGCACAAGGTCTAACTTTCTTGCATGAAGAAGGGCCTTTTCAGgtacaactat ... ttgtctgcagGCAATGTATAATGAGTTCTCAACAGCCAACATACAGATTGACAAAGATTTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttattaggttaactacacatgttatctttgctgacatccttatttttgtctgcagGCAATGTATAATGAGTTCTCAACAGCCAACATACAGATTGACAAAGATTTCAGTGCAAAGCTTTCAGGATATGGTTGTGTTGGACATATTCCCGAGGAAG
tgctgac putative branch site (score: 2)
tccttatttttgtct CT-rich tract
ttatttttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atttgtttttcgtagtatggagtgaatgatttcaagatgttatgattattaggttaactacacatgttatctttgctgacatccttatttttgtctgcagGCAATGTATAATGAGTTCTCAACAGCCAACATACAGATTGACAAAGATTTCAGTGCAAAGCTTTCAGGATATGGTTGTGTTGGACATATTCCCGAGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - -tggagtg
- - - - - - - - - - - - - - - - - - -tgttatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctacaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgac