Sequence
atgc intronic sequence ATGC exonic sequence...tcatgtttgttgagaatcagaataggatcagtttcagattgatgcaaaagctttttacttttcacataactgataattttttgttactaatgttctacagGCAGATTTGGTGGGATGTCCAGTAATTAGACCTGCTGACATAGAGACAACAGCACTTGGAGCAGCCTATGCTGCCGGATTAGCTACTGGGATTTGGAAAG
Basic information
species | Glycine max |
transcript | GLYMA07G03230.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G03230.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os04g55410.1 (Oryza sativa), 3'ss of exon 3
----tcatgtttgttgagaatcagaataggatcagtttcagattgatgcaaaagctttttac-ttttcacataactgataattttttgttactaatgttctacagGCAGATTTGGTGGGATGTCCAGTAATTAGACCTGCTGACATAGAGACAACAGCACTTGGAGCAGCCTATGCTGCCGGATTAGCTACTGGGATTTGGAAAG
| || | | || | || | | | | | || |||| || | | || || | | | ||||| | | || ||||| ||||| |||| | || || | |||||||||||||| |||||||| || |||||||| || ||||| || ||||||||| ||| | |||
ggtgtaattgtagctgtagcttagtgaaacgtttctctttg-caattgtaaaatctctccaaattcccataagatcactgattttgcatgcaca----cctgcagGCTGATTTATTGGGTAGCCCTGTTGTCAGACCTGCTGACATCGAGACAACTGCCCTTGGAGCTGCGTATGCAGCTGGATTAGCTGTTGGAGTCTGGTCGA
upper sequence: GLYMA07G03230.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G80460.2 (Arabidopsis thaliana), 3'ss of exon 3
tcatgtttgttgagaatcagaataggatcagtttcagattgatgcaaaagcttt-ttacttttcacataactgataattttttgttactaatgttctacagGCAGATTTGGTGGGATGTCC----AGTAATTAGACCTGCTGACATAGAGACAACAGCACTTGGAGCAGCCTATGCTGCCGGATTAGCTACTG-----GGATTTGGAAAG--
| |||| ||| ||| | | | | | | | | | || | | | | || | | | | | ||| |||| | || | | | || || |||| | | | | || | || | || | || | | | | || |||| | ||| | | |||
------tccttgaaaat-gttgcaggctgatctgatgggaagtccggtggtgaggccagtggacatagagacaacagcattagg--agcagc-ctatgcagctggattagCTGTGGGATTCTGGAAGGAAGCAGACATATTCGAGTCGGGAGAGAAG-GCGAAGAACT-CCAAAGTTTTCAGACCCGCTATGGAAGAAGGAATCAGGAAGAA
upper sequence: GLYMA07G03230.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G80460.1 (Arabidopsis thaliana), 3'ss of exon 3
tcatgtttgttgagaatcagaa-taggatcagtttcagattgatgcaaaagctttt-tacttttcacataactgataattttttgttact---aatgttctacagGCAGATTTGGTGGGATGTCCAGTAATTAGACCTGCTGACATAGAGACAACAGCACTTGGAGCAGCCTATGCTGCCGGATTAGCTACTGGGATTTGGAAAG
|| || ||| || | || || | | ||| | | | || | | || |||| | | | | | || | | || | | ||||| ||| || ||||| |||| || | || || | |||||||||||||||||| | |||||||||||||| || ||||||||| || | ||||| |
----gtatgatgatgctctcctctcttctctgtatgaatcagattctgatgattgtgttgttcgaacattaatctcattctcttatctccttgaaaatgttgcagGCTGATCTGATGGGAAGTCCGGTGGTGAGGCCAGTGGACATAGAGACAACAGCATTAGGAGCAGCCTATGCAGCTGGATTAGCTGTGGGATTCTGGAAGG
upper sequence: GLYMA07G03230.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv09s0002g07860.t01 (Vitis vinifera), 3'ss of exon 3
----tcatgtttgttgagaatcagaataggatcagtttcagattgatgcaaaagctttttacttttcacataactgataattttttgttactaatgttctacagGCAGATTTGGTGGGATGTCCAGTAATTAGACCTGCTGACATAGAGACAACAGCACTTGGAGCAGCCTATGCTGCCGGATTAGCTACTGGGATTTGGAAAG
||||| |||| | | | | || | | || | | ||| | | | ||| ||||| ||| |||||| | | ||||| ||| || |||| || || ||||||| ||||| |||||||||||||| |||||||| || ||||| || |||||||| |||||||||| ||
gtcttcatgcttgtggtatcttatatcag-actgcccataatcccatactgtccttgtttgaactgttta-atttgacaatttgctgt--ctaatgatttgcagGCTGATCTGTTGGGGAACCCGGTGGTTAGACCAGCTGATATAGAGACAACAGCTCTTGGAGCCGCTTATGCAGCTGGATTAGCAGTGGGGATTTGGACAG
upper sequence: GLYMA07G03230.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv09s0002g07640.t01 (Vitis vinifera), 3'ss of exon 2
----tcatgtttgttgagaatcagaataggatcagtttcagattgatgcaaaagctttttacttttcacataactgataattttttgttactaatgttctacagGCAGATTTGGTGGGATGTCCAGTAATTAGACCTGCTGACATAGAGACAACAGCACTTGGAGCAGCCTATGCTGCCGGATTAGCTACTGGGATTTGGAAAG
||||| |||| | | | | || | | || | | ||| | || ||| ||||| ||| |||||| | | ||||| ||| || |||| || || ||||||| ||||| |||||||||||||| |||||||| || ||||| || |||||||| |||||||||| ||
gtcttcatgcttgtggtatcttatatcag-actgcccataatcccatactgtccttgtttgaactgttt-tatttgacaatttgctgt--ctaatgatttgcagGCTGATCTGCTGGGGAACCCGGTGGTTAGACCAGCTGATATAGAGACAACAGCTCTTGGAGCCGCTTATGCAGCTGGATTAGCAGTGGGGATTTGGACAGMapped 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|254326616|gb|GR841208.1|GR841208EST: TTAGAGTGGATGGTGGGGCAACTGTAAACAACCTGCTGATGCAGATTCAG GCAGATTTGGTGGGATGTCCAGTAATTAGACCTGCTGACATAGAGACAACA
genomic: TTAGAGTGGATGGTGGGGCAACTGTAAACAACCTGCTGATGCAGATTCAGgtttggacta ... tgttctacagGCAGATTTGGTGGGATGTCCAGTAATTAGACCTGCTGACATAGAGACAACA
EST:
gi|208159049|gb|GD951774.1|GD951774EST: ACAACCTGCTGATGCAGATTCAG GCAGATTTGGTGGGATGTCCAGTAATTAGACCTGCTGACATAGAGACAACA
genomic: ACAACCTGCTGATGCAGATTCAGgtttggacta ... tgttctacagGCAGATTTGGTGGGATGTCCAGTAATTAGACCTGCTGACATAGAGACAACA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaagctttttacttttcacataactgataattttttgttactaatgttctacagGCAGATTTGGTGGGATGTCCAGTAATTAGACCTGCTGACATAGAGACAACAGCACTTGGAGCAGCCTATGCTGCCGGATTAGCTACTGGGATTTGGAAAG
tactaat putative branch site (score: 1)
ataattttttgttact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcatgtttgttgagaatcagaataggatcagtttcagattgatgcaaaagctttttacttttcacataactgataattttttgttactaatgttctacagGCAGATTTGGTGGGATGTCCAGTAATTAGACCTGCTGACATAGAGACAACAGCACTTGGAGCAGCCTATGCTGCCGGATTAGCTACTGGGATTTGGAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- -tgtttgt
- - - - - - - - - - - - - - - - - - - -tgatgca