Sequence
atgc intronic sequence ATGC exonic sequence...tcacaataaaatttaatcgtttatatttattcattttcctctcgacatgataaaattcatctctttgatgatacttccccttttgatgatgtgtataaagCCATCCAAACGCAGTTGGTATATGGTCAAGAGAGCAAATCGAAGCATGGAAACCCATTGTGGATGCTGTTCATGCCAAAGGTGGTATATTCTTCTGTCAG
Basic information
species | Glycine max |
transcript | GLYMA13G25570.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G25570.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0041g02080.t01 (Vitis vinifera), 3'ss of exon 2
--------------------------------------tcacaataaaatttaatcgtttatatttattcattttcctctcgacatgataaaattcatctc------------tttgatgata-cttccccttttgatga------tgtgtataaagCCATCCAAACGCAGTTGGTATATGGTCAAGAGAGCAAATCGAAGCATGGAAACCCATTGTGGATGCTGTTCATGCCAAAGGTGGTATATTCTTCTGTCAG
|| ||| ||| | || | | | | || | | | | | | ||| || | || | || | ||| | |||| || | | | || |||| | || || |||||| ||| ||| ||| | |||||||||||||| ||||| |||||||| ||||| ||||| ||||| || || ||||||
gtacttgtagaagtcattttctgaagttccattcattttctaaatgaaaataaacaaaatgtgctcaagcacatactctccagtgttttgatattgatgttggccctttcaatttcgttgttttcttttctttttttcgaattttccatatttttagGTATCCCCATACACCGGGCATATGGACAAAAGAACAAGTTGAAGCATGGAAACCTATTGTCGATGCTGTACATGCTAAAGGCGGTATCTTTTTTTGTCAG
upper sequence: GLYMA13G25570.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0041g02050.t01 (Vitis vinifera), 3'ss of exon 1
----tcacaataaaatttaatcgtttatatt-tattcattttcc---tctcgaca---------tgataaaattcatctctttgatgatacttccccttttgatgatgtgtataaagCCATCCAAACGCAGTTGGTATATGGTCAAGAGAGCAAATCGAAGCATGGAAACCCATTGTGGATGCTGTTCATGCCAAAGGTGGTATATTCTTCTGTCAG
| ||| ||| || | | | || | ||||||||| | | | | |||| || || || | | | || || | || | | ||| ||| || || | | ||||||||| ||| ||||||| | ||||| ||||| |||||||| |||||||||||||| ||||| |||| || | ||||||
gtaattacagcaaacactactttctcaacttctgttcattttctaagtttaaataaaaaatatatgatcaagttgatagatataagattaattatctggtttttcccatctatgtagCTATGCACATACCCCGGGTATATGGACAAAAGAGCAAGTTGAAGCCTGGAAGCCCATTGTAGATGCTGTTCATGCTAAAGGCAGTATCTTTATTTGTCAG
upper sequence: GLYMA13G25570.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0041g02040.t01 (Vitis vinifera), 3'ss of exon 3
tcacaataaaatttaatcgtttatatttattcattttcctctcgacatgataaaattcatctctttgatgatacttccccttttgatgatgtgtataaagCCATCCAAACGCAGTTGGTATATGGTCAAGAGAGCAAATCGAAGCATGGAAACCCATTGTGGATGCTGTTCATGCCAAAGGTGGTATATTCTTCTGTCAG-------------------------------
|||||||| ||| ||||||| | ||||| ||||| |||||||| |||||||||||||| ||||| |||| || | ||||||
---------------------------------------------------------------------------------------------------------------------gtatatggacaaaagagcaagttgaagcctggaagcccattgtagatgctgttcatgctaaaggcagtatctttatttgtcagCTTTGGCATGTGGGAAGAGTTTCAAACACAG
upper sequence: GLYMA13G25570.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0041g02070.t01 (Vitis vinifera), 3'ss of exon 2
tcacaataaaatttaatcgtttatatttattcattttcctctcgacatgataaaattcatctctttgatgatacttccccttttgatgatgtgtataaagCCATCCAAACGCAGTTGGTATATGGTCAAGAGAGCAAATCGAAGCATGGAAACCCATTGTGGATGCTGTTCATGCCAAAGGTGGTATATTCTTCTGTCAG
|||| | | || |||| || | | || | || | | | |||| | |||||| | || ||| || || | | ||||||||| ||| ||||||| | ||||| ||||| |||||||| |||||||||||||| ||||| |||| || | ||||||
-------gtaattacagcaaatacttttaccttcttgtgttttgatagatgtaagattaattatttggt----tttccccacct----------atgcagCTATGCACATACCCCGGGTATATGGACAAAAGAGCAAGTTGAAGCCTGGAAGCCCATTGTAGATGCTGTTCATGCTAAAGGCAGTATCTTTATTTGTCAG
upper sequence: GLYMA13G25570.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0041g02010.t01 (Vitis vinifera), 3'ss of exon 2
----tcacaataaaatttaatcgtttatatt-tattcattttcc---tctcgaca----------tgataaaattcatctctttgatgatacttccccttttgatgatgtgtataaagCCATCCAAACGCAGTTGGTATATGGTCAAGAGAGCAAATCGAAGCATGGAAACCCATTGTGGATGCTGTTCATGCCAAAGGTGGTATATTCTTCTGTCAG
| ||| ||| || | | | || | ||||||||| | | | | |||| ||||| || | | | || || | || | | ||| ||| || || | | ||||||||| ||| ||||||| | ||||| ||||| |||||||| |||||||||||||| ||||| |||| || ||||||
gtaattacagcaaacactactttctcaacttctgttcattttctaagtttaaataaaaaaatatatgatcaaattgatagatataagattaattatctggtttttcccatctatgtagCTATGCACATACCCCGGGTATATGGACAAAAGAGCAAGTTGAAGCCTGGAAGCCCATTGTAGATGCTGTTCATGCTAAAGGCAGTATCTTTAATTGTCAG
upper sequence: GLYMA13G25570.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0041g02060.t01 (Vitis vinifera), 3'ss of exon 2
---------------------------------------------------------tcacaataaaatttaatcgtttatatttattc----attttcctctcgacatgataaaattcatctctttgatgatacttccccttttga---tgatgtgtataaagCCATCCAAACGCAGTTGGTATATGGTCAAGAGAGCAAATCGAAGCATGGAAACCCATTGTGGATGCTGTTCATGCCAAAGGTGGTATATTCTTCTGTCAG
| ||||| | ||| | || ||| |||| | | || | || | | | | || || || ||| || | | | | || ||||||| || || |||||| ||| ||| ||| | ||||| |||||||| ||||| |||||||||||||| ||||| ||||| || || ||||||
gtaattgtagaagaagtcattttctgaagttccattcattttctaaatgaaaaaaaaaaaatgcaaaatgtgctcgagcacatactttccagtgttttgatattgatgttggccctgtcgtttttgttattttattttatttttggaattttccatatttttagGTATCCAAATACACCAGGCATATGGACAAAAGAACAAGTTGAAGCTTGGAAACCTATTGTAGATGCTGTTCATGCTAAAGGCGGTATCTTTTTTTGTCAG
upper sequence: GLYMA13G25570.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0041g02020.t01 (Vitis vinifera), 3'ss of exon 2
-------------------------------------------------------------tcacaataaaatttaatcgtttatatttattcattttcctctcgacatgataaaattcatctctttgatgatacttccccttttgatgatgtgtataa----agCCATCCAAACGCAGTTGGTATATGGTCAAGAGAGCAAATCGAAGCATGGAAACCCATTGTGGATGCTGTTCATGCCAAAGGTGGTATATTCTTCTGTCAG
| | | | || | | || || || | | | | | || | | ||| | || | ||||| | | ||| || ||||| | || || |||||| ||| ||| ||| | |||||||||||||| ||||| |||||||| ||||| ||||| ||||| || || ||||||
gtaattgtagaagaagtcattttctgaagttccattccttttctaaatgaaaataaacaaaatgtgctcgagcacatactttccagtgttttgatattgatgttggccctgtcgtttttgtttttttattttcttttttctttttggaattttccatatttttagGTATCCACATACACCAGGCATATGGACAAAAGAACAAGTTGAAGCATGGAAACCTATTGTAGATGCTGTACATGCTAAAGGCGGTATCTTTTTTTGTCAG
upper sequence: GLYMA13G25570.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ23431 (Selaginella moellendorffii), 3'ss of exon 2
tcacaataaaatttaatcgtttatatttattcattttcctctcgacatgataaaattcatctctttgatgatacttccccttttgatgatgtgtataaagCCATCCAAACGCAGTTGGTATATGGTCAAGAGAGCAAATCGAAGCATGGAAACCCATTGTGGATGCTGTTCATGCCAAAGGTGGTATATTCTTCTGTCAG
|| | | | ||| || || | | | | || | | | | | || |||| | ||| || ||||| |||||| |||||||||||||||| ||||| | |||||||||| |||||| | | | ||||| |||
-----------------------------------------gtga-aagctgttcttcctccattctcttgttttactgaattgcaagcttggatttcagATATCCGCATAGCCCTGGAATCTGGTCCGAGGAGCAAGTCGAAGCATGGAAACCGATTGTCCAGGCTGTTCATGACAAAGGAGCTGTTTTCTTTCTACAGMapped 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|37994582|gb|CF806278.1|CF806278EST: GGAGGTCTTCTGATTACTGAAGCTACTACTATTTCACCCACTTCTAAATA CCATCCAAACGCAGTTGGTATATGGTCAAGAGAGCAAATCGAAGCATGGAA
genomic: GGAGGTCTTCTGATTACTGAAGCTACTACTATTTCACCCACTTCTAAATAgtacgtaatt ... gtgtataaagCCATCCAAACGCAGTTGGTATATGGTCAAGAGAGCAAATCGAAGCATGGAA
EST:
gi|151401890|gb|EV271703.1|EV271703EST: GGAGGTCTTCTGATTACTGAAGCTACTACTATTTCACCCACTTCTAAATA CCATCCAAACGCAGTTGGTATATGGTCAAGAGAGCAAATCGAAGCATGGAA
genomic: GGAGGTCTTCTGATTACTGAAGCTACTACTATTTCACCCACTTCTAAATAgtacgtaatt ... gtgtataaagCCATCCAAACGCAGTTGGTATATGGTCAAGAGAGCAAATCGAAGCATGGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catgataaaattcatctctttgatgatacttccccttttgatgatgtgtataaagCCATCCAAACGCAGTTGGTATATGGTCAAGAGAGCAAATCGAAGCATGGAAACCCATTGTGGATGCTGTTCATGCCAAAGGTGGTATATTCTTCTGTCAG
ttttgat putative branch site (score: 4)
taaaattcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcacaataaaatttaatcgtttatatttattcattttcctctcgacatgataaaattcatctctttgatgatacttccccttttgatgatgtgtataaagCCATCCAAACGCAGTTGGTATATGGTCAAGAGAGCAAATCGAAGCATGGAAACCCATTGTGGATGCTGTTCATGCCAAAGGTGGTATATTCTTCTGTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - aataaaa
- - - - - - - - - - - - - - - - - - tcctctc
- - - - - - - - - - - - - - - - - - - - - -gacatga