Sequence
atgc intronic sequence ATGC exonic sequence...tatattagtatttatattcattagcataattttaaactccctattttctatgtagcttgaattaggacctgtatgttcttaatagattattattttgtagAAATAGGAGCAACATGGCCTATACTCCTTGGTGGCCAAGCTCATTGGACAGTTGGTCTTGTGGTAACTTTGATTACCATAAGCAGCGTAATTGCAGCTGA
Basic information
species | Glycine max |
transcript | GLYMA11G30030.3 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G30030.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g03460.1 (Oryza sativa), 3'ss of exon 2
----------------tatattagtatttatattcattagcataattttaaactccctattttctatgtagcttg-aattaggacctgtatgttcttaatagattattattttgtagAAATAGGAGCAACATGGCCTATACTCCTTGGTGGCCAAGCTCATTGGACAGTTGGTCTTGTGGTAACTTTGATTACCATAAGCAGCGTAATTGCAGCTGA
| | ||| || || || | ||| ||| | |||| | |||| | | ||||| | | | || | | ||| |||||| | | | ||||| ||||| |||||||| |||||||| ||||||||||| ||||| | ||| |||||| | || || ||
ggttcataaaaagttgagcagcaaagtttttaccagtt--caagagtttgtactgttaaatttcactatagcaagcgaataggattcctcttgcttatgcagTATGTGTTTTGCCAGAAATTGCATACAGTTGGCCAATACTTCTTGGTGGGCAAGCTCACTGGACAGTTGGACTTGTAGCAACCTTGATTTCTATTAGTAG---------------
upper sequence: GLYMA11G30030.2 (Glycine max), 3'ss of exon 4
lower sequence: AT2G45150.2 (Arabidopsis thaliana), 3'ss of exon 3
--------------tatattagtatttatattcattagcat--aattttaaactccctattttctatgtagcttgaattaggacctgtatgttcttaatagatt-----attattt-tgtagAAATAGGAGCAACATGGCCTATACTCCTTGGTGGCCAAGCTCATTGGACAGTTGGTCTTGTGGTAACTTTGATTACCATAAGCAGCGTAATTGCAGCTGA
| | | ||||||| | | | ||| | | || | ||| | | | || || | | | | | || ||| ||| | ||| || ||| |||||||| || || |||||||| |||||||||||||||||||| ||||||| ||| |||||| | | ||| | |||||||| | ||
gcaagctctcgccttttctcctcttttatatctctaaagttcagattattgaggccaagctctctgctttgtcctacttcagatgtccttttgaccagttttttttcctattgtttctatagGTATCGGAAGGACATGGCCAATTCTTCTTGGTGGTCAAGCTCATTGGACAGTTGGACTTGTGGCAACATTGATTTCTTTCAGCGGTGTAATTGCGACAGA
upper sequence: GLYMA11G30030.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv15s0048g00240.t01 (Vitis vinifera), 3'ss of exon 3
-tatattagtatttatattcattagcataattttaaactccctattttctatgtagcttgaattaggacctgtatgttcttaatagattattattttgtagAAATAGGAGCAACATGGCCTATACTCCTTGGTGGCCAAGCTCATTGGACAGTTGGTCTTGTGGTAACTTTGATTACCATAAGCAGCGTAATTGCAGCTGA
| | | || | || ||| | | | | | | || | || | | | | | | || | || | | ||| |||| ||||||| | | |||||| | || |||||||| ||||||||||||||||| |||||||||||||| |||||| | || ||||| |||||||||| ||
gaacacctgcatgtgggcccac-agctttgtgtatattctgagcctgtggatctgctttatgctttgccagctgtttcctaaccagggttatttttggtagGAATAGGAACGGCTTGGCCTTTTCTTCTTGGTGGTCAAGCTCATTGGACAGTGGGTCTTGTGGTAACCTTGATTTCTATCAGCAGTATAATTGCAGCAGAMapped 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|19937553|gb|BQ081336.1|BQ081336EST: TTTCTGGGTTAAACTTCGATGTAGTTTAGCAGCTCCAGCCTTGAATACAA AAATAGGAGCAACATGGCCTATACTCCTTGGTGGCCAAGCTCATTGGACAG
genomic: TTTCTGGGTTAAACTTCGATGTAGTTTAGCAGCTCCAGCCTTGAATACAAgtaattgact ... tattttgtagAAATAGGAGCAACATGGCCTATACTCCTTGGTGGCCAAGCTCATTGGACAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctatgtagcttgaattaggacctgtatgttcttaatagattattattttgtagAAATAGGAGCAACATGGCCTATACTCCTTGGTGGCCAAGCTCATTGGACAGTTGGTCTTGTGGTAACTTTGATTACCATAAGCAGCGTAATTGCAGCTGA
tcttaat putative branch site (score: 3)
ttatttt putative PPT
tatgttcttaatagat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatattagtatttatattcattagcataattttaaactccctattttctatgtagcttgaattaggacctgtatgttcttaatagattattattttgtagAAATAGGAGCAACATGGCCTATACTCCTTGGTGGCCAAGCTCATTGGACAGTTGGTCTTGTGGTAACTTTGATTACCATAAGCAGCGTAATTGCAGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA