Sequence
atgc intronic sequence ATGC exonic sequencegtatatttttttgcttagttatctctttgtctaatttcttaatttaaattttaaagactagctgaaaatggagctttatatttgacatttggtgcctttgttttgcagTCATCCTATGGATTCATTCATTACTTTGATCGCAGATCTGCTGCTCTTGCCATATTATCTCTCAATGGAAGGCATCT
Basic information
species | Glycine max |
transcript | GLYMA07G04640.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G04640.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM5G835213_T02 (Zea mays), 3'ss of exon 3
gtatatttttttgcttagttatctctttgtctaatttcttaatttaaattttaaagactagctgaaaatggagctttatatttgacatttggtgcctttgttttgcagTCATCCTATGGATTCATTCATTACTTTGATCGCAGATCTGCTGCTCTTGCCATATTATCTCTCAATGGAAGGCATCT
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--atgtgttaattgttaatgatttatgtagattttcttatcctttatatattaaattgtttatggcaatgtgatctta------acactttctgttctgatgttgcagTCATCCTTTGGTTTCATTGACTACTATGACCGCAGATATGCTGCACTAGCAATTTTATCTCTCAATGGCAGACAACT
upper sequence: GLYMA07G04640.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G008611_T01 (Zea mays), 3'ss of exon 4
gtatatttttttgcttagttatctctttgtctaatttctta--atttaaattttaaagactagctgaaaatggagctttatatttgacatttggtgcctttgttttgcagTCATCCTATGGATTCATTCATTACTTTGATCGCAGATCTGCTGCTCTTGCCATATTATCTCTCAATGGAAGGCATCT
| | || | ||| | || | | || || ||||||| ||||| || ||||| | || |||| | ||||| ||| || || || | ||||||||||||| ||| |||||| | ||| ||||||||||| |||||| || || || |||||||||||||| || || ||
---tgtgttaattgttaatgatttact-gtatattttcttatcatttatatattaaattgtttatggcaatg-----tgatatt-aacactttctgttttgatgttgcagTCATCCTTTGGTTTCATTGACTACCATGATCGCAGATATGCTGCACTAGCAATTTTATCTCTCAATGGCAGACAACT
upper sequence: GLYMA07G04640.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G17370.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatatttttttgcttagttatctctttgtctaatttcttaatttaaattttaaagacta--gctgaaaatggagcttt--atatttgacat--ttggtgcctttgttt--tgcagTCATCCTATGGATTCATTCATTACTTTGATCGCAGATCTGCTGCTCTTGCCATATTATCTCTCAATGGAAGGCATCT
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gtgtgttatgttacacttttataacattctagtagtaatcttcaggatgtttaatcttttatgttgaaacttttgcttttggtattggctatgattgacacatttatctgatgcagTCTTCTTATGGGTTTGTGCACTACTTTGATCGAAGATCGGCTGGTCTTGCAATCCTTTCTCTCAATGGAAGGCATTT
upper sequence: GLYMA07G04640.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G14100.1 (Arabidopsis thaliana), 3'ss of exon 3
-------------------------------------------------------------gtatatttttttgcttagttatctctttgtc--taatttcttaatttaaat--tttaaaga-----------------ctagctgaaaatggagctttatatttgacatttggtgcctttgttttgcagTCATCCTATGGATTCATTCATTACTTTGATCGCAGATCTGCTGCTCTTGCCATATTATCTCTCAATGGAAGGCATCT
||| ||| || || | | || |||| | | ||| ||| ||||| || || || |||||||| || | ||| | | || |||||||||||| |||||||| |||| ||||||||||| ||||| |||||||| || ||| | ||||| || |||||||||||
gtagttagattctaaaatccacctgatttctactttattgtgaaagtgaccctcttatatagtagctttcttgttttggacgagcatacctcaacaattgcacatttttaatactttaaggaaactactctacttgctgcttactaaaaatggactcataaagcatgcatct--ttttatttatttgcagTCATCATATGGATTTGTTCACTACTTTGATCGAAGATCCGCTGCTCTGGCTATACTGTCTCTGAACGGAAGGCATCT
upper sequence: GLYMA07G04640.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G54080.2 (Arabidopsis thaliana), 3'ss of exon 3
gtatatttttttgcttagttatctctttgtctaatttcttaatttaaattttaaagactagc---tgaaaatggagctttatatttgacatttggtgcctttgttttgcagTCATCCTATGGATTCATTCATTACTTTGATCGCAGATCTGCTGCTCTTGCCATATTATCTCTCAATGGAAGGCATCT
||| | |||| | | | ||| | | | ||| | |||| | | ||||| | | || | ||| || | | | ||||||||||||| |||||||| |||| ||||||||||| |||| |||| | | || ||| | |||| || ||||||||| |
gtagagttttgga---acccgcccttctgttttttattcgaatgaagcttttcggtagtgttctttgaaagctaacttctagacatga-atgttttacac---ttttgcagTCATCATATGGATTTGTTCACTACTTTGATCGAAGATGTGCTAGTATGGCTATAATGACTCTTAACGGAAGGCATAT
upper sequence: GLYMA07G04640.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0002g00880.t01 (Vitis vinifera), 3'ss of exon 3
-----------------------------------------------------gtatatttttttgcttagttatctctttgtctaatttcttaatttaaattttaaagactagct--gaaaatggagctttatatttgacattt--ggtgcctttgttt--tgcagTCATCCTATGGATTCATTCATTACTTTGATCGCAGATCTGCTGCTCTTGCCATATTATCTCTCAATGGAAGGCATCT
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gtatattcttctttatgctatcttgttaatttttggattgtacctgttaagctgaagatctgtatggaaaagttattagacttctcacatgttagtttagcattctatcccttactttgctggtttatcatcatatt-gacatctccattgattctcctcggtgcagTCATCCTATGGATTCATCCACTACTTTGATCGCAGATCTGCTGCATTGGCTATATTGTCTCTAAACGGAAGGCATCTMapped 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|7146716|gb|AW508638.1|AW508638EST: TCTCGGGTACTGGCCCAGTTGAAGGTTGTAAGCTTATCAGAAAGGATAAG TCATCCTATGGATTCATTCATTACTTTGATCGCAGATCTGCTGCTCTTGCC
genomic: TCTCGGGTACTGGCCCAGTTGAAGGTTGTAAGCTTATCAGAAAGGATAAGgtatattttt ... tgttttgcagTCATCCTATGGATTCATTCATTACTTTGATCGCAGATCTGCTGCTCTTGCC
EST:
gi|208032967|gb|GD830024.1|GD830024EST: CTTATCAGAAAGGATAAG TCATCCTATGGATTCATTCATTACTTTGATCGCAGATCTGCTGCTCTTGCC
genomic: CTTATCAGAAAGGATAAGgtatattttt ... tgttttgcagTCATCCTATGGATTCATTCATTACTTTGATCGCAGATCTGCTGCTCTTGCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagactagctgaaaatggagctttatatttgacatttggtgcctttgttttgcagTCATCCTATGGATTCATTCATTACTTTGATCGCAGATCTGCTGCTCTTGCCATATTATCTCTCAATGGAAGGCATCT
atttgac putative branch site (score: 4)
cctttgtttt putative PPT
tttatatttgacattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatatttttttgcttagttatctctttgtctaatttcttaatttaaattttaaagactagctgaaaatggagctttatatttgacatttggtgcctttgttttgcagTCATCCTATGGATTCATTCATTACTTTGATCGCAGATCTGCTGCTCTTGCCATATTATCTCTCAATGGAAGGCATCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG