Sequence
atgc intronic sequence ATGC exonic sequencegttattatgggcataagaattaatttccatgacaacattttggttttttagaccttgtaattgataagattatttcaattcttgaatccagGTTGGAGGGGATTGCTTATAAGGTACTTCAGTGGTATTTATGTAGACTGGAGGGCTGGTTTGCTGCAGACACTGATGCTATTTCACTGAAAGGATGGGAC
Basic information
species | Glycine max |
transcript | GLYMA08G41570.3 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G41570.3 (Glycine max), 3'ss of exon 6
lower sequence: Vv12s0028g01120.t01 (Vitis vinifera), 3'ss of exon 6
gttattatgggcataagaattaatttccatgacaacattttggttttttagaccttgtaattgataa--gattattt--caattcttgaatccagGTTGGAGGGGATTGCTTATAAGGTACTTCAGTGGTATTTATGTAGACTGGAGGGCTGGTTTGCTGCAGACACTGATGCTATTTCACTGAAAGGATGGGAC
|| || || | | ||||| || | | | | | | || | | |||| | || ||| | || | | ||| |||| |||||||| | ||| |||||||||| || ||||| || || ||| |||| ||||||||||||||||| ||||| || ||||| ||| | |||||
--gttttccatcacaacactagatttcaat---agcctgctaaatatatatatttcttaatagtcaatagatgacttagtatatacaaaatgcagGCTGGAGGGGCTGGCTCATAAGGTACTGCAATGGTACTTGTGCAGAATGGAAGGCTGGTTTGCTGCAGATGCTGATAACATATCACTTAAAAGTTGGGAT
upper sequence: GLYMA08G41570.3 (Glycine max), 3'ss of exon 6
lower sequence: EFJ33019 (Selaginella moellendorffii), 3'ss of exon 8
gttattatgggcataagaattaatttccatgacaacattttggttttttagaccttgtaattgataagattatttcaattcttgaatccagGTTGGAGGGGATTGCTTATAAGGTACTTCAGTGGTATTTATGTAGACTGGAGGGCTGGTTTGCTGCAGACACTGATGCTATTTCACTGAAAGGATGGGAC
| || | || | | | | | || | ||| || || | | | || | |||||||| |||||||||||||| || ||||||||||| ||| | ||| || || || | |||||
--------------------------------------------gtacgagctttcctactccgacttagcactaaatatccctgtttcagACAAGAAGGCCTGGGACACCGAGTTTTACAGTGGTACTTATGTAGACTGGAAGGATGGTTTGCTGCTGACGCAGATAAAATCTCCCTCCAGAACTGGGAT
upper sequence: GLYMA08G41570.3 (Glycine max), 3'ss of exon 6
lower sequence: EFJ30336 (Selaginella moellendorffii), 3'ss of exon 5
gttattatgggcataagaattaatttccatgacaacattttggttttttagaccttgtaattgataagattatttcaattcttgaatccagGTTGGAGGGGATTGCTTATAAGGTACTTCAGTGGTATTTATGTAGACTGGAGGGCTGGTTTGCTGCAGACACTGATGCTATTTCACTGAAAGGATGGGAC
| || | || | | | | | || | ||| || || | | | || | |||||||| |||||||||||||| || ||||||||||| ||| | ||| || || || | | |||||
--------------------------------------------gtacgagctttcctactccgacttagcactaaatatccctgtttcagACAAGAAGGCCTGGGACACCGAGTTTTACAGTGGTACTTATGTAGACTGGAAGGATGGTTTGCTGCTGACGCAGATAAAATCTCCCTCCAGAGCTGGGATMapped 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|7673728|gb|AW160135.1|AW160135EST: TCTGTACTTCGTGGTCTTTCAATCGTTTTCGATAGGAAGCCAGAACTGAG GTTGGAGGGGATTGCTTATAAGGTACTTCAGTGGTATTTATGTAGACTGGA
genomic: TCTGTACTTCGTGGTCTTTCAATCGTTTTCGATAGGAAGCCAGAACTGAGgttattatgg ... ttgaatccagGTTGGAGGGGATTGCTTATAAGGTACTTCAGTGGTATTTATGTAGACTGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attttggttttttagaccttgtaattgataagattatttcaattcttgaatccagGTTGGAGGGGATTGCTTATAAGGTACTTCAGTGGTATTTATGTAGACTGGAGGGCTGGTTTGCTGCAGACACTGATGCTATTTCACTGAAAGGATGGGAC
aattgat putative branch site (score: 4)
ttctt putative PPT
taattgataagattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttattatgggcataagaattaatttccatgacaacattttggttttttagaccttgtaattgataagattatttcaattcttgaatccagGTTGGAGGGGATTGCTTATAAGGTACTTCAGTGGTATTTATGTAGACTGGAGGGCTGGTTTGCTGCAGACACTGATGCTATTTCACTGAAAGGATGGGAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG