Sequence
atgc intronic sequence ATGC exonic sequence...aacataatgaagggctatccttttaaactataggcaaagtgatgttgagaaatatctgttgattagtgatcatctgactttactacctcttgtactgcagGAACATTTGTTAATAGTATGTGAACTACTTAAAGCCAATTTATATGAGTTTCACAAATTTAATCGAGAATCAGGGGGGGAAGTGTATTTCACGATGCCAA
Basic information
species | Glycine max |
transcript | GLYMA16G34510.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G34510.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G015073_T01 (Zea mays), 3'ss of exon 3
aacataatgaagggctatccttttaaactataggcaaagtgatgttgagaaatatctgttgattagtgatcatctgactttactacctcttgta--------ctgcagGAACATTTGTTAATAGTATGTGAACTACTTAAAGCCAATTTATATGAGTTTCACAAATTTAATCGAGAATCAGGGGGGGAAGTGTATTTCACGATGCCAA
| | | | | | | | | | || || ||| | | | |||||| || | || | |||||||||||||| | ||||| |||||||| || || || ||| | ||||||||||| ||||| || ||||||||||||| || || || ||||| |||||||
--------ggaatttcagagctcagggttgataattggttcttttccaaagcaatttgccttaaagtcacaacatttctttaccacttatttcaaatactgtttgcagGAACATTTGCTGATAGTCTGTGAACTTCTGAAGGCAAATCTGTATGAGTTTCAGAAATTCAACAGAGAATCAGGGGGTGAGGTTTACTTCACAATGCCAA
upper sequence: GLYMA16G34510.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G73450.1 (Arabidopsis thaliana), 3'ss of exon 3
--------------------------------------------------------------------------------------aacataatgaagggc--tatccttttaaactataggcaaagtgatgttgagaaatatctgttgattagtgatcatctgactttactacctcttgtactgcagGAACATTTGTTAATAGTATGTGAACTACTTAAAGCCAATTTATATGAGTTTCACAAATTTAATCGAGAATCAGGGGGGGAAGTGTATTTCACGATGCCAA
| || || | | ||| | ||| | || | | || || | | ||| || ||| | | || | || | || | ||||||| || ||| |||| ||||||||||| ||||| |||||| |||| ||||| ||||||||||| |||||||||| || ||||| ||||||||||||||||
gtaagtgattacatcccttttgcaaaatttggttttgctactgtatatcaaaagtgaccaattgtgtctttctcttcaacaattttagcacaagtgtgaaccatatgccttttatttaatacctttgcaatatttctctttgtggattgtttggtg--taacggattcc-ctgaatgttct-ttgcagGAGCACTTGCTAATTGTATGTGAACTTCTTAAGGCCAATCTATACGAGTTCCACAAATTTAACAGAGAATCAGGTGGTGAAGTTTATTTCACGATGCCAA
upper sequence: GLYMA16G34510.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G17750.1 (Arabidopsis thaliana), 3'ss of exon 4
-----------------------------------------------------------------aacataatgaagggctatccttttaa---actataggcaaagtgatgttgagaaatatctgttgattagtgatcatctgactttactacctcttgtactgcagGAACATTTGTTAATAGTATGTGAACTACTTAAAGCCAATTTATATGAGTTTCACAAATTTAATCGAGAATCAGGGGGGGAAGTGTATTTCACGATGCCAA
|||| | | || | | || || | | || || | ||| | ||| | || | ||| || ||||||| || ||||||||||||||||||| || || || || || |||||||| || || |||||| | ||||||||||| || || |||||||| |||||||
gtaagtagatagatgcagaattgtatctttttcttttcaacaccgggtggatattctgctgctttggtgctatgatgtatcaattgttcgattcagtaaagaacatgggacgtgagcctacatcatgatgccattgactgtgattaattggaatctca-gttttgcagGAGCACCTGTTAATAGTATGTGAACTTCTCAAGGCAAACTTGTATGAGTTCCAAAAGTTTAATAGGGAATCAGGGGGAGAGGTTTATTTCACTATGCCAA
upper sequence: GLYMA16G34510.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G73460.1 (Arabidopsis thaliana), 3'ss of exon 3
aacataatgaagggctatccttttaaactataggcaaagtgatgttgagaaatatct--gttgattagtgatcatc-tgactttactacctcttgtactgcagGAACATTTGTTAATAGTATGTGAACTACTTAAAGCCAATTTATATGAGTTTCACAAATTTAATCGAGAATCAGGGGGGGAAGTGTATTTCACGATGCCAA
| ||| | | || | |||||| | | | | || | || ||| || |||| | | | || || | || | ||||||| || ||| |||| ||||||||||| ||||| |||||| |||| || || ||||||||||| |||||||||| || ||||| ||||||||||||||||
attgaaatataaaggggtcataataaact--aagtaggtttgcattattatatctctttgtggattgtttggtgtaacggattccctgaatgttct-ttgcagGAGCACTTGCTAATTGTATGTGAACTTCTTAAGGCCAATCTATACGAATTCCACAAATTTAACAGAGAATCAGGTGGTGAAGTTTATTTCACGATGCCAA
upper sequence: GLYMA16G34510.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv01s0011g01590.t01 (Vitis vinifera), 3'ss of exon 9
---aacataatgaagggctatcctttta-aactataggcaaagtgatgttgagaaatatctgttgattagtgatcatctgactttactacctcttgtactgcagGAACATTTGTTAATAGTATGTGAACTACTTAAAGCCAATTTATATGAGTTTCACAAATTTAATCGAGAATCAGGGGGGGAAGTGTATTTCACGATGCCAA
|| | | ||| | |||| | | ||| | || | | ||| | | | | ||| || |||||| | || | ||||||||||||| ||||| ||||| ||||| || || || || || ||||||||||| ||||||||| ||||||| || ||||| || || ||||| |||||||
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|24137018|gb|BU927528.1|BU927528EST: CTTCAGACAAGTACCACCTTCTAAGATTGTATGATTACTTCTATTATAGA GAACATTTGTTAATAGTATGTGAACTACTTAAAGCCAACTTATATGAGTTT
genomic: CTTCAGACAAGTACCACCTTCTAAGATTGTATGATTACTTTTATTATAGAgtaagtgaat ... tgtactgcagGAACATTTGTTAATAGTATGTGAACTACTTAAAGCCAATTTATATGAGTTT
EST:
gi|6567092|gb|AW234719.1|AW234719EST: CTTCAGACAAGTACCACCTTCTAAGATTGTATGATTACTTTTATTATAGA GAACATTTGTTAATAGTATGTGAACTACTTAAAGCCAATTTATATGAGTTT
genomic: CTTCAGACAAGTACCACCTTCTAAGATTGTATGATTACTTTTATTATAGAgtaagtgaat ... tgtactgcagGAACATTTGTTAATAGTATGTGAACTACTTAAAGCCAATTTATATGAGTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgagaaatatctgttgattagtgatcatctgactttactacctcttgtactgcagGAACATTTGTTAATAGTATGTGAACTACTTAAAGCCAATTTATATGAGTTTCACAAATTTAATCGAGAATCAGGGGGGGAAGTGTATTTCACGATGCCAA
atctgac putative branch site (score: 3)
ctttactacctctt CT-rich tract
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aacataatgaagggctatccttttaaactataggcaaagtgatgttgagaaatatctgttgattagtgatcatctgactttactacctcttgtactgcagGAACATTTGTTAATAGTATGTGAACTACTTAAAGCCAATTTATATGAGTTTCACAAATTTAATCGAGAATCAGGGGGGGAAGTGTATTTCACGATGCCAA
- - -aatgaag
- - - - - - - - - - - - - - - - - - - - gatgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - tctgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catctga