Sequence
atgc intronic sequence ATGC exonic sequencegtaagtttctttcttgtcactaattatctttgaactttatcctgtgctcttctccatataccactttgcaatggcattgattctctgttgattcccttttcagCTGGGAAATCATCTGTTCTGTTGGATGTGAAACCATGGGACGATGAAACTGACATGAAGAAGCTCGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTT
Basic information
species | Glycine max |
transcript | GLYMA06G17930.3 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G17930.4 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os07g42300.2 (Oryza sativa), 3'ss of exon 5
--------------------------------------------------gtaagt--ttctttcttgtcactaattatctttgaactttatcctgtgctcttctccatataccactttgcaa--tggcattgattctctgttgattccctttt---cagCTGGGAAATCATCTGTTCTGTTGGATGTGAAACCATGGGACGATGAAACTGACATGAAGAAGCTCGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTT
| | | || | | || | | | | || | ||| || || | || | | ||||| || | | | ||| | || |||| |||||||||| || || || || | ||||| ||||||||||||||||| |||||||||| || | |||||||| ||||| |||| |||||||||| |
gtatgccatcctgcattatactataccatttttatgcaatgaataatacaattattcattttattttattctcatctgtagctgtaaattaagaccaaatcatcactattcattataatgcaaagtgctacttctaacttgtcaacacctttttattcagCTGGGAAGTCCTCAGTGTTGCTTGATGTCAAACCATGGGACGATGAGACTGACATGACCAAATTGGAAGAAGCTGTGAGGAATGTTAAGATGGAAGGCCT
upper sequence: GLYMA06G17930.4 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g29260.1 (Oryza sativa), 3'ss of exon 5
gtaagtttctttcttgtcactaattatctttgaactttatcctgtgctcttc--tccatataccactttgcaatggcattgattctctgttgattccct-tttcagCTGGGAAATCATCTGTTCTGTTGGATGTGAAACCATGGGACGATGAAACTGACATGAAGAAGCTCGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTT
| | | | | | | ||| | || | | |||| | | ||| | | |||| | || ||| | || | | ||| ||||||||||||||| |||||| | ||||| || |||||||| || ||||| |||||| ||||| || ||||| ||||| ||| ||||||| || |
-----catttatgctattagccccaaaatttaatattgaggcaatgctatatgatatataaaaaatattgccaaaa-atctattactaacttatcctttattttagCTGGGAAATCATCGGTTCTGCTAGATGTAAAGCCATGGGATGACGAAACAGACATGGCAAAGCTTGAGGAAGCTGTGAGGAATGTGAAGATGGAGGGCCT
upper sequence: GLYMA06G17930.4 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G031545_T03 (Zea mays), 3'ss of exon 5
--------------------------------------------------------------gtaagtttctttcttgtcactaatt-atctttgaactttatcctgt-gctcttctccatatacca--ctttgcaatggcattgattctctgttgattcccttttcagCTGGGAAATCATCTGTTCTGTTGGATGTGAAACCATGGGACGATGAAACTGACATGAAGAAGCTCGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTT
| ||| | || ||| | | | | | | | || ||||| | |||| | | ||| || ||| || ||| | || | || ||||||||||| ||||| ||| | | |||||||| |||||||||||||| ||||||||| |||||||| ||||| || || ||| |||||||||||| |
gtatgtcagtgtgcatattttttctgtttcattctctcatcacactgtgttgacatgtgctgacactaatctataatgacacccttggaccactatatcgttttttgaagctctgtttgatatccaaaaacttgtgatttcatcaatcttctttccataca-ttgtcagCTGGGAAGTCATCAGTTTTACTTGATGTGAAGCCATGGGACGATGAGACTGACATGGCCAAGCTCGAGGAAGCTGTTAGGAGTGTCCAGATGGAAGGGCT
upper sequence: GLYMA06G17930.4 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G153569_T02 (Zea mays), 3'ss of exon 5
-------------------gtaagtttctttcttgtcactaattatctttg--aactttatcctgt-------gctcttctccatataccactttgcaatggcattgattct--ctgttgattcccttttcagCTGGGAAATCATCTGTTCTGTTGGATGTGAAACCATGGGACGATGAAACTGACATGAAGAAGCTCGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTT
| |||| |||| | | | | ||| | ||| ||| ||| | | |||| | | | |||| | |||| | || | |||| |||||||||||||| || ||| | | |||||||| |||||||||||||| ||||||||| |||||||| ||||| || || ||| ||||||||||| |
gtatgtcagtgtgcatagtttctgttttattctctcaatcacacacccttgctattgctatattgttgttgaggctttgtttcatacccaaaagctttaaagcat-ggttctaacctttccataccttgtcagCTGGGAAATCGTCAGTTTTACTTGATGTGAAGCCATGGGACGATGAGACTGACATGGCCAAGCTCGAGGAAGCTGTTAGGAGTGTCCAGATGGAAGGACT
upper sequence: GLYMA06G17930.4 (Glycine max), 3'ss of exon 5
lower sequence: AT2G18110.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaagtttctttcttgtcactaattatctttgaactttatcctgtgctcttctccata-taccactttgcaatgg-cattgattctctgttgattcccttttcagCTGGGAAATCATCTGTTCTGTTGGATGTGAAACCATGGGACGATGAAACTGACATGAAGAAGCTCGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTT
|| | | | | |||| || ||||| | | | ||| | ||| | | ||| | ||| || || | | ||||| || || ||||| ||| || ||||| | || || ||||| ||||| || |||||||||||||| || ||||| || ||||| ||||||||||||| ||
---------------gtaagtttgtgtttttgcctttacacctgtagtttacgatataatgatgtcttggatttctcatctggtttct-ttcttttcttaatcagCCGGAAAGTCATCAGTTTTGATGGATATCAAGCCGTGGGATGATGAGACGGACATGAAGAAGCTAGAGGAAGCTGTAAGATCCATTCAGATGGAAGGATT
upper sequence: GLYMA06G17930.4 (Glycine max), 3'ss of exon 5
lower sequence: AT1G30230.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaagtttctttcttgtcactaattatctttgaactttatcctgtgctcttctccatataccactttgcaatggcattgattctctgttgattcccttttcagCTGGGAAATCATCTGTTCTGTTGGATGTGAAACCATGGGACGATGAAACTGACATGAAGAAGCTCGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTT
|||||||| | |||| || | ||| | ||||| | | | | ||| | | ||||| | | | || | | | | |||||| || || || ||| || | ||| | ||||| ||||| ||||| ||||||||||||||||| || ||||| |||| || ||||||||||||| ||
gtaagtttgggttttgtt-----ctacccttgtaatttatatgaa----tgatatgaagatgtcttggatttctcattg--tttttatta--ttcttcattagCTGGAAAGTCCTCAGTTTTGATTGATATCAAACCGTGGGATGATGAGACTGACATGAAGAAGCTTGAGGAAGCTGTGAAGTCCATTCAGATGGAAGGTTT
upper sequence: GLYMA06G17930.4 (Glycine max), 3'ss of exon 5
lower sequence: Vv17s0000g01540.t01 (Vitis vinifera), 3'ss of exon 5
gtaagtttctttcttgtcactaattatctttgaactttatcctgtgctcttctccatataccactttgcaatggcattgattctctgt-tgattcccttttcagCTGGGAAATCATCTGTTCTGTTGGATGTGAAACCATGGGACGATGAAACTGACATGAAGAAGCTCGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTT
|| | ||| || ||| ||| | || | | || | | || ||| || | ||| | | | || | || |||||||| || || || ||| |||||||||||||||||||||| ||||| ||||||||||| ||||| || |||||||| | || | |||||||||||
----attattgagatgtacctgcctatatttcttttaaatatgggtcctctcctactttccctttttagcataatctgaattttatttgtgtgtttattctcagCTGGCAAGTCTTCAGTTTTGTTGGATGTGAAACCATGGGATGATGAGACTGACATGAAAAAGCTTGAGGAAGCAGTACGTAGCATTAAAATGGAAGGGTT
upper sequence: GLYMA06G17930.4 (Glycine max), 3'ss of exon 5
lower sequence: EFJ07795 (Selaginella moellendorffii), 3'ss of exon 4
gtaagtttctttcttgtcactaattatctttgaactttatcctgtgctcttctccatataccactttgcaatggca-ttgattctctgttgattcccttttcagCTGGGAAATCATCTGTTCTGTTGGATGTGAAACCATGGGACGATGAAACTGACATGAAGAAGCTCGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTT
| ||||| | || | | |||| || ||| | | | | |||||||||||| || || || |||| ||||||||||||||||||||||| |||||| ||||||||| | || ||||| | || || ||| ||| |
------------------------------------------------gtaagccata-gcttctcttctatggttcttcgagctcactctctcttttgtatagCTGGGAAATCGTCCGTGCTTATGGACGTGAAACCATGGGACGATGAAACCGACATGGTGAAGCTCGAGGCGGCTGTGAGGGCCGTGCAAATGCCCGGGCT
upper sequence: GLYMA06G17930.4 (Glycine max), 3'ss of exon 5
lower sequence: EFJ28248 (Selaginella moellendorffii), 3'ss of exon 4
gtaagtttctttcttgtcactaattatctttgaactttatcctgtgctcttctccatataccactttgcaatggcattgattctctgttgattcccttttcagCTGGGAAATCATCTGTTCTGTTGGATGTGAAACCATGGGACGATGAAACTGACATGAAGAAGCTCGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTT
| | || ||| ||| | ||| | | | | | | ||||| || | | |||||||||||| || || || |||| ||||||||||||||||||||||| |||||| ||||||||| | || ||||| | || || ||| ||| |
-----------------------------------gtaagccatagcttctcttc-tatttggttcttcga----gctcactctctctt------ttgtatagCTGGGAAATCGTCCGTGCTTATGGACGTGAAACCATGGGACGATGAAACCGACATGGTGAAGCTCGAGGCGGCTGTGAGGGCCGTGCAAATGCCCGGGCTMapped 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|9259946|gb|BE348093.1|BE348093EST: AGCAGAGGAACGGGCAACTGCAGTGAAGGCATCTACAAAANAAAAAGAGT CTGGGAAATCATTCTGT-CTGGTGGATGGGAAACCATGG
genomic: AGCAGAGGAACGGGCAGCTGCAGTGAAGGCATCTACAAAAAAAAAAGAGTgtaagtttct ... cccttttcagCTGGGAAATCAT-CTGTTCTGTTGGATGTGAAACCATGG
EST:
gi|208112180|gb|GD912851.1|GD912851EST: ATCT-CAAANAAAAAAGAGT CTGGGAAATCATCTGTTCTGTTGGATGTGAAACCATGGGACGATGAAACTG
genomic: ATCTACAAAAAAAAAAGAGTgtaagtttct ... cccttttcagCTGGGAAATCATCTGTTCTGTTGGATGTGAAACCATGGGACGATGAAACTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttctccatataccactttgcaatggcattgattctctgttgattcccttttcagCTGGGAAATCATCTGTTCTGTTGGATGTGAAACCATGGGACGATGAAACTGACATGAAGAAGCTCGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTT
tgttgat putative branch site (score: 4)
ttctctgttgattccc CT-rich tract
attgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtttctttcttgtcactaattatctttgaactttatcctgtgctcttctccatataccactttgcaatggcattgattctctgttgattcccttttcagCTGGGAAATCATCTGTTCTGTTGGATGTGAAACCATGGGACGATGAAACTGACATGAAGAAGCTCGAAGAAGCAGTGAGATCTGTTCAGATGGAAGGGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG