Sequence
atgc intronic sequence ATGC exonic sequencegtatgtctgcattttattattcccttttgaaagtattatgttttgtctgtcttttcttgtttgtaataatgcattagtgatttgatgatctgggctcttatttaagcgagtgttcatatgaatttgcagCTGAGTAGTTGCTTCCTTGTGTGCATGAAAGATGATAGTATAGAGGGGATATATGAAACTTTGAAGGAGTGTGCTATCATCAGCAAATCAGCTGGAGGAA
Basic information
species | Glycine max |
transcript | GLYMA06G15350.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G15350.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os06g07210.1 (Oryza sativa), 3'ss of exon 4
gtatgtctgcattttattattcccttttgaaagtattatgttttgtctgtcttttcttgtttgtaataatgcattagtgatttgatgatctgggct--cttatttaagcgagtgttcatatgaatttgcagCTGAGTAGTTGCTTCCTTGTGTGCATGAAAGATGATAGTATAGAGGGGATATATGAAACTTTGAAGGAGTGTGCTATCATCAGCAAATCAGCTGGAGGAA
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-------------------------------------------------gtactgcacatttg-accagaaaaatcctagtcttggactctgaaattgcttgcttactcttttattctctgcaat--gcagTTAAGCAGCTGTTTCCTTATCTGCATGAAAGATGACAGCATTGAGGGAATCTATGATACTTTGAAGGAATGTGCTGTCATAAGCAAATCTGCTGGAGGAA
upper sequence: GLYMA06G15350.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G340527_T01 (Zea mays), 3'ss of exon 4
gtatgtctgcattttattattcccttttgaaagtattatgttttgt-ctgtcttttcttgtttgtaataatgcattagtgatttgatgatctgggctcttatttaagcgagtgttcatatgaatttgcagCTGAGTAGTTGCTTCCTTGTGTGCATGAAAGATGATAGTATAGAGGGGATATATGAAACTTTGAAGGAGTGTGCTATCATCAGCAAATCAGCTGGAGGAA
|| ||||||| | | | ||| | ||| |||| | | ||| ||| || | ||| ||||| | || || || || ||| | |||||||||||||| || || ||||| || |||||||| |||||||||||||| | || |||||||||||||||||||
--------------------------------------------gtactgtcttgcttcctgccagacgatgtcattgtgggttgaaattgt------ttacttactgtttcttttctgtga---tgcagTTAAGCAGCTGTTTTCTTATATGCATGAAAGATGACAGCATTGAGGGAATCTATGAAACCCTGAAGGAGTGTGCTGTAATAAGCAAATCAGCTGGAGGAA
upper sequence: GLYMA06G15350.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G304362_T01 (Zea mays), 3'ss of exon 4
gtatgtctgcattttattattcccttttgaaagtattatgttttgt-ctgtcttttcttgtttgtaataatgcattagtgatttgatgatctgggctcttatttaagcgagtgttcatatgaatttgcagCTGAGTAGTTGCTTCCTTGTGTGCATGAAAGATGATAGTATAGAGGGGATATATGAAACTTTGAAGGAGTGTGCTATCATCAGCAAATCAGCTGGAGGAA
|| ||||||| | | || ||| | ||| || | || ||| | || | || | ||| ||||| | || || || || ||| | |||||||||||||| || || ||||| || |||||||| |||| ||||||||| | || |||||||| ||||||||||
--------------------------------------------gtactgtcttgtttcccgccagatgatgtcattgtgggttctgaaattgtttatttact---gctgctttttctgtga---tgcagTTAAGCAGCTGTTTTCTTATATGCATGAAAGATGACAGCATTGAGGGAATCTATGAAACCCTGAAAGAGTGTGCTGTAATAAGCAAATCTGCTGGAGGAA
upper sequence: GLYMA06G15350.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv07s0031g01990.t01 (Vitis vinifera), 3'ss of exon 4
-----------------------------gtatgtctgcattttattattcccttttgaaagtattatgttttgtctgtcttttc--ttgtttgt--aataatgcattag-------tgatttgatgatctg----ggctcttatttaagcgagtgttca--tatgaatttgcagCTGAGTAGTTGCTTCCTTGTGTGCATGAAAGATGATAGTATAGAGGGGATATATGAAACTTTGAAGGAGTGTGCTATCATCAGCAAATCAGCTGGAGGAA
||| | | ||| | | ||||| | || | ||| | | || | ||| |||| |||| |||| || || | | | || || | | |||||| |||| | ||||||||||| ||||||||| | |||||||||||||||||||| || || |||||||| ||| | |||||||||||| | |||||||| || ||||||||||
gtatgtttcacacgcacatgaactagattttatataacttgtccattttcctctttttcttatgtttttatttattacttttattagttgattgtggaatatgctgttaggatcctttgcttgaacagtgtacattggtctttgctaatttctgtgttctgttatgtgctgacagCTGAGTAGCTGCTTCCTTATTTGCATGAAAGATGATAGTATTGAAGGAATATATGACACTCTAAAGGAGTGTGCTGTTATCAGCAAGTCTGCTGGAGGAA
upper sequence: GLYMA06G15350.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S195_46V6.1 (Physcomitrella patens), 3'ss of exon 3
-------gtatgtctgcattttatt--attcccttttgaaagtattatgttttgtctgtcttttcttgtttgtaataatgcattagtgatttgatgatctgggctcttatttaagcgagtgttcatatgaatttgcagCTGAGTAGTTGCTTCCTTGTGTGCATGAAAGATGATAGTATAGAGGGGATATATGAAACTTTGAAGGAGTGTGCTATCATCAGCAAATCAGCTGGAGGAA
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gtaggacttgcgttccaattcaactggatgccatggttgcaattttttattttattttgttttacttcttccctcttg---gtgggcggtgtaatggaaggtacttatacctggcttggtgttc----gggcgtccagCTGAGCAGTTGCTTCCTTGTATGCACCAAAGGCGACAGCATTGAGGGTATCTACGACACTCTGAAGGAGTGTGCTGTTATTAGCAAGTCAGCTGGTGGAA
upper sequence: GLYMA06G15350.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S64_38V6.1 (Physcomitrella patens), 3'ss of exon 3
gtatgtctgcattttattattcccttttgaaagtattatgttttgtctgt-cttttcttgtttgtaataatgcattagtgatttgatgatctgggctcttatttaagcgagtgttcatatgaatttgcagCTGAGTAGTTGCTTCCTTGTGTGCATGAAAGATGATAGTATAGAGGGGATATATGAAACTTTGAAGGAGTGTGCTATCATCAGCAAATCAGCTGGAGGAA
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-----------------------gttcggctatctattccttttgtgcgtgcgctctttgcactgaaccaagc-ctggtcagtcgtgaatgcgagtactaatt-----ggttgttcgaatg---ttgcagCTAAGCAGCTGTTTCCTACTGTGCATGAAAAATGACAGTATTGAGGGGATTTACGATACCCTGAAGGAGTGTGCTGTAATTAGCAAGTCGGCCGGTGGCAMapped 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|208090328|gb|GD885349.1|GD885349EST: TCACCCATGCATCTCCGACACTTTTCAATGCTGGAACACCTAGGCCTCAA CTGAGTAGTTGCTTCCTTGTGTGCATGAAAGATGATAGTATAGAGGGGATA
genomic: TCACCCATGCATCTCCGACACTTTTCAATGCTGGAACACCTAGGCCTCAAgtatgtctgc ... gaatttgcagCTGAGTAGTTGCTTCCTTGTGTGCATGAAAGATGATAGTATAGAGGGGATA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagtgatttgatgatctgggctcttatttaagcgagtgttcatatgaatttgcagCTGAGTAGTTGCTTCCTTGTGTGCATGAAAGATGATAGTATAGAGGGGATATATGAAACTTTGAAGGAGTGTGCTATCATCAGCAAATCAGCTGGAGGAA
atttgat putative branch site (score: 5)
tcttatttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtctgcattttattattcccttttgaaagtattatgttttgtctgtcttttcttgtttgtaataatgcattagtgatttgatgatctgggctcttatttaagcgagtgttcatatgaatttgcagCTGAGTAGTTGCTTCCTTGTGTGCATGAAAGATGATAGTATAGAGGGGATATATGAAACTTTGAAGGAGTGTGCTATCATCAGCAAATCAGCTGGAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA