Sequence
atgc intronic sequence ATGC exonic sequencegtatgtgtaataataacttgagggaaatgatatgtcatatatattgtctattttcttctgttaattctcagttgtgtttccccccctatcgtgttctactcctcagGTGAATCCCATTGCTGTAAATAGTAAGTACTGTAATGTCTTCACGGAGAACAAGAGAGTTATTTCAAGAATTTCAACTGTAGATTTTGGAAAG
Basic information
species | Glycine max |
transcript | GLYMA15G05680.1 |
intron # | 18 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G05680.1 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM2G133885_T02 (Zea mays), 3'ss of exon 2
-------------------------gtatgtgtaataataacttgagggaaatgatatgtcatatatattgtctattttcttctgttaattctcagttgtgtttccccccctatcgtgttctactcctcagGTGAATCCCATTGCTGTAAATAGTAAGTACTGTAATGTCTTCACGGAGAACAAGAGAGTTATTTCAAGAATTTCAACTGTAGATTTTGGAAAG
| ||| | | || || ||||||| | | || | | | | ||| | ||||||| | | | || | | | |||||||||||||| ||||| ||||| ||||| || ||||| ||||| ||||| || |||||| | |||| || |||||| ||| |||||||||
gtatataatacttatatcggcacgctttgatgtcactgtggtaactggaaagggatatgtt---tgtgttctgctctatttcttgtcatttctcagc-atctgctgatgctggtctacctgcatttgacagGTGAATCCCATCGCTGTGAATAGCAAGTATTGCAATGTATTCACTGAGAATAAAAGAGTTGTATCAATGATATCAACTTCAGAGTTTGGAAAG
upper sequence: GLYMA15G05680.1 (Glycine max), 3'ss of exon 18
lower sequence: AT5G57190.1 (Arabidopsis thaliana), 3'ss of exon 17
gtatgtgtaataataacttgagggaaatgatat--gtcatatatattgtctattttcttctgttaattctcagttgtgtttccccccctatcgtgttctactcctcagGTGAATCCCATTGCTGTAAATAGTAAGTACTGTAATGTCTTCACGGAGAACAAGAGAGTTATTTCAAGAATTTCAACTGTAGATTTTGGAAAG
|||||| | || | | | | | ||| | || | ||| | || | |||||| | | | | | |||| | |||| ||||| ||||| || ||||| |||||||||||||| |||||||| || || || || ||| || ||||| | ||| |||||||||
gtatgtagttatgcatctcctctgcatttactttagtccaagatttcctctcatctccctcatgttttctcatgagactcacttttgtttccttgttgaat-----agGTTAATCCAATTGCGGTCAATAGCAAGTACTGTAATGTATTCACGGAAAATAAACGAACCGTTGCAATTATATCAACAGCAGAATTTGGAAAG
upper sequence: GLYMA15G05680.1 (Glycine max), 3'ss of exon 18
lower sequence: AT4G25970.1 (Arabidopsis thaliana), 3'ss of exon 17
gtatgtgtaataataacttgagggaaatgatatgtcatatatattgtc--tattttcttctgttaattctcagttgtgtttccccccctatcgtgttctactcctcagGTGAATCCCATTGCTGTAAATAGTAAGTACTGTAATGTCTTCACGGAGAACAAGAGAGTTATTTCAAGAATTTCAACTGTAGATTTTGGAAAG
| | | || | ||| | | | | || ||||| |||| || ||| || | |||| | | | ||||||| ||||| |||||||| ||||| |||||||||||||| ||||| ||||| || | || || || ||||| | ||| |||||||||
-----------------gtattgcatctgccttttcacgttgaagagcattcttctcttccgttattttcttattggagttacttttgtatcct----tggttctcagGTTAATCCGATTGCTGTCAATAGCAAGTACTGTAATGTGTTCACTGAGAATAAACGGACCATCGTAATTATATCAACAGCAGAGTTTGGAAAG
upper sequence: GLYMA15G05680.1 (Glycine max), 3'ss of exon 18
lower sequence: Vv12s0055g00710.t01 (Vitis vinifera), 3'ss of exon 14
gtatgtgtaataataacttgagggaaatgatat--gtcatatatattgtctattttcttctgttaattctcagttgtgtttccccccctatcgtgttctactcctcagGTGAATCCCATTGCTGTAAATAGTAAGTACTGTAATGTCTTCACGGAGAACAAGAGAGTTATTTCAAGAATTTCAACTGTAGATTTTGGAAAG
||||||| ||| || | || | || | || | || | | | ||| | ||| |||| | || || | | | ||| |||| || |||| |||||||||||||| ||||| ||||| || ||||| ||||| ||||||||| |||| | || |||||||| ||||||||| |||
gtatgtgcaattattatctgttgaaattcatgtttgttttgcaaactgtttttttgtttcttcagaacttcccatg-atcttttactttatttctttctgct----agGTTAATCCCATTGCTGTGAATAGCAAGTATTGCAATGTATTCACAGAGAACAAGCGAGTAGTATCTGTTATTTCAACATCAGATTTTGGGAAG
upper sequence: GLYMA15G05680.1 (Glycine max), 3'ss of exon 18
lower sequence: EFJ07899 (Selaginella moellendorffii), 3'ss of exon 16
gtatgtgtaataataacttgagggaaatgatatgtcatatatattgtctattttct-tctgttaattctcagttgtgtttccccccctatcgtgttctactcctcagGTGAATCCCATTGCTGTAAATAGTAAGTACTGTAATGTCTTCACGGAGAACAAGAGAGTTATTTCAAGAATTTCAACTGTAGATTTTGGAAAG
|| | ||| | | | || | | | ||||| |||| | | || | ||||||||||| ||||| || |||||| ||| |||||||| |||||||| |||||| | | | ||| | ||||| | || |||||||||| ||
---------------------------------------------gtatggcctctgtgaggtgatgcataaac-tatttcc-----tatcttatact--tttgcagGTGAATCCTATTGCCGTGAATAGTCCGTATTGTAATGTTTTCACGGACAACAAGCGCGCTGTTTGCATCATTTCTAGTGAAGATTTTGGACAG
upper sequence: GLYMA15G05680.1 (Glycine max), 3'ss of exon 18
lower sequence: EFJ07241 (Selaginella moellendorffii), 3'ss of exon 16
gtatgtgtaataataacttgagggaaatgatatgtcatatatattgtctattttcttctgttaattctcagttgtgtttccccccctatcgtgttctactcctcagGTGAATCCCATTGCTGTAAATAGTAAGTACTGTAATGTCTTCACGGAGAACAAGAGAGTTATTTCAAGAATTTCAACTGTAGATTTTGGAAAG
||| ||| ||| | | | | |||||| | | || | ||||||||||| ||||| || |||||| ||| |||||||| |||||||| |||||| | | | ||| | ||||| | || |||||||||| ||
-----------------------------------------------gtatggcctt-tgtgaggtgatg--cataaattatttcctatcttatact--tttgcagGTGAATCCTATTGCCGTGAATAGTCCGTATTGTAATGTTTTCACGGACAACAAGCGCGCTGTTTGCATCATTTCTAGTGAAGATTTTGGACAGMapped 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|7029617|gb|AW459334.1|AW459334EST: TATCAGGAATTTTTGAGCAATCTGTAGATATCCCTGGATGCTTGTATACT GTGAATCCCATTGCTGTAAATAGTAAGTACTGTAATGTCTTCACGGAGAAC
genomic: TATCAGGAATTTTTGAGCAATCTGTAGATATCCCTGGATGCTTGTATACTgtatgtgtaa ... tactcctcagGTGAATCCCATTGCTGTAAATAGTAAGTACTGTAATGTCTTCACGGAGAAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttcttctgttaattctcagttgtgtttccccccctatcgtgttctactcctcagGTGAATCCCATTGCTGTAAATAGTAAGTACTGTAATGTCTTCACGGAGAACAAGAGAGTTATTTCAAGAATTTCAACTGTAGATTTTGGAAAG
tgttaat putative branch site (score: 3)
tttccccccctatcgt putative PPT
tgttaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtgtaataataacttgagggaaatgatatgtcatatatattgtctattttcttctgttaattctcagttgtgtttccccccctatcgtgttctactcctcagGTGAATCCCATTGCTGTAAATAGTAAGTACTGTAATGTCTTCACGGAGAACAAGAGAGTTATTTCAAGAATTTCAACTGTAGATTTTGGAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA