Sequence
atgc intronic sequence ATGC exonic sequencegtttgatccttgtgtcctgcattttttaaattttttttattttgggccttatttttcgcattgcaattatgtatgtggccggaaaaattgtgatatttataagtatttgaatttgggaatttgatcagCATTCTTTACAACCGTGGAGTTTATCCAGAAGAAAGCTTTGTGAAGGTTAAGAAATATGGCCTCCCCATGTTGCTTACTGAAGATGAGGGTGTCAAAACT
Basic information
species | Glycine max |
transcript | GLYMA11G37380.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G37380.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G25980.1 (Arabidopsis thaliana), 3'ss of exon 2
gtttgatccttgtgtcctgcattttttaaattttttttattttgggccttatttttcgcattgcaattatgtatgtggccggaaaaattgtgatatttataagtatttgaatttgggaatttgatcagCATTCTTTACAACCGTGGAGTTTATCCAGAAGAAAGCTTTGTGAAGGTTAAGAAATATGGCCTCCCCATGTTGCTTACTGAAGATGAGGGTGTCAAAACT
||| ||| | | | | |||| || ||| | | | | || || || ||| | | | | |||||| ||| | |||| | | |||| | ||| || | || || |||| |||||||||||| ||||| |||||||| || ||||||||||| || || |||||||||| ||||||||| |||||| ||
--gtgagaattg-gatcggaacttttcaa--tttcagtgtctggaa----atcttcgattctgtgattttttt-----acagtgaaattg----attcgt---tattggtttctgggta------cagTATATTGTATAATCGTGCAGTTTATCCAGAGGAAAGTTTTGTGAAAGTGAAGAAATATGGACTTCCGATGTTGCTTATTGAAGATGAATCCGTCAAATCT
upper sequence: GLYMA11G37380.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G25980.2 (Arabidopsis thaliana), 3'ss of exon 1
gtttgatccttgtgtcctgcattttttaaattttttttattttgggccttatttttcgcattgcaattatgtatgtggccggaaaaattgtgatatttataagtatttgaatttgggaatttgatcagCATTCTTTACAACCGTGGAGTTTATCCAGAAGAAAGCTTTGTGAAGGTTAAGAAATATGGCCTCCCCATGTTGCTTACTGAAGATGAGGGTGTCAAAACT
||| ||| | | | | |||| || ||| | | | | || || || ||| | | | | |||||| ||| | |||| | | |||| | ||| || | || || |||| |||||||||||| ||||| |||||||| || ||||||||||| || || |||||||||| ||||||||| |||||| ||
---tgagaattg-gatcggaacttttcaa--tttcagtgtctggaa----atcttcgattctgtgattttttt-----acagtgaaattg----attcgt---tattggtttctgggta------cagTATATTGTATAATCGTGCAGTTTATCCAGAGGAAAGTTTTGTGAAAGTGAAGAAATATGGACTTCCGATGTTGCTTATTGAAGATGAATCCGTCAAATCT
upper sequence: GLYMA11G37380.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv01s0010g02430.t01 (Vitis vinifera), 3'ss of exon 2
gtttgatccttgtgtcctgcattttttaaattttttttattttgggccttatttttcgcattgcaattatgtatgtggccggaaaaattgtgatatttataagtatttgaatttgggaatttgatcagCATTCTTTACAACCGTGGAGTTTATCCAGAAGAAAGCTTTGTGAAGGTTAAGAAATATGGCCTCCCCATGTTGCTTACTGAAGATGAGGGTGTCAAAACT
|| ||| | || | | || |||| | || ||| | || || | |||||| || || || ||| ||||| || || | | ||| || |||| ||||| ||||| || ||||||||||| |||||| |||| || || |||||||||||||| || ||| |||||||| ||||||||||||| ||| |
gtatgaacattaaaa--taaacggattgaattgtagtttatttaattttctgttgaatttttagatttatgtttg-ggttgggaaa---gtgattttgatgggaa----------agaaaatgttcagTATTCTATACAATCGCGGAGTTTATCCGGAAGAATCTTTTGGAAAAGTGAAGAAATATGGCCTTCCAATGCTGCTTACTCAAGATGAGGGTGTTAAATCGMapped 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|21595080|gb|BQ610361.1|BQ610361EST: AGTTCTTCGGATATGCTGCTAACAG CATTCTTTACAACCGTGGAGTTTATCCAGAAGAAAGCTTTGTGAAGGTTAA
genomic: AGTTCTTCGGATATGCTGCTAACAGgtttgatcct ... atttgatcagCATTCTTTACAACCGTGGAGTTTATCCAGAAGAAAGCTTTGTGAAGGTTAA
EST:
gi|24206284|gb|BU965537.1|BU965537EST: AGTTCTTCGGATATGCTGCTAACAG CATTCTTTACAACCGTGGAGTTTATCCAGAAGAAAGCTTTGTGAAGGTTAA
genomic: AGTTCTTCGGATATGCTGCTAACAGgtttgatcct ... atttgatcagCATTCTTTACAACCGTGGAGTTTATCCAGAAGAAAGCTTTGTGAAGGTTAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtggccggaaaaattgtgatatttataagtatttgaatttgggaatttgatcagCATTCTTTACAACCGTGGAGTTTATCCAGAAGAAAGCTTTGTGAAGGTTAAGAAATATGGCCTCCCCATGTTGCTTACTGAAGATGAGGGTGTCAAAACT
aaaaattgtgatattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgatccttgtgtcctgcattttttaaattttttttattttgggccttatttttcgcattgcaattatgtatgtggccggaaaaattgtgatatttataagtatttgaatttgggaatttgatcagCATTCTTTACAACCGTGGAGTTTATCCAGAAGAAAGCTTTGTGAAGGTTAAGAAATATGGCCTCCCCATGTTGCTTACTGAAGATGAGGGTGTCAAAACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG