Sequence
atgc intronic sequence ATGC exonic sequence...aagataattccttcctggaagccactaattaggtcttattgaataaatgacacatttttagattgatgcttatctatgattatgttgtgctatttgcagcCAATGTTTCCCGGAGAGAGTGGGGTTGATCAATTGGTAGAGATCATTAAGG
Basic information
species | Glycine max |
transcript | GLYMA18G45960.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G45960.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S306_62V6.1 (Physcomitrella patens), 3'ss of exon 6
aagataattccttcctggaagccactaattaggtcttattgaataaatgacacatttttagattgatgcttatctatgattatg-ttgtgctat--ttgcagcCAATGTTTCCCGGAGAGAGTGGGGTTGATCAATTGGTAGAGATCATTAAGG
|| || || ||| || | | || | | ||| | |||| | | || | ||| | | || || | |||||||| ||||||| ||||||||||| || ||||||||||| || ||||| |||
--gacgatatgttgctgtggcgcaagtgtagaggtttgaagttgaggtgagggagctttatgtgtaatctgggttttgacgacgcttttgatgggattgcagCCTTTGTTTCCTGGAGAGAGTGGAGTGGATCAATTGGTGGAAATCATCAAG-
upper sequence: GLYMA18G45960.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S60_85V6.1 (Physcomitrella patens), 3'ss of exon 7
aagataattccttcctggaagccactaattag-gtcttattgaataaatgacacatttttag-attgatgcttatctatgattatgttgtgc---tatttgcagcCAATGTTTCCCGGAGAGAGTGGGGTTGATCAATTGGTAGAGATCATTAAGG
| | | || | | | | | ||| | | | || | | || | | |||| | | ||| | || || | |||||||| |||| |||||||||||||| || ||||||||||| ||||| || |||
---accacatgtgtgtgtgtgttgcaagtcggagtcatggagtttgggcgagtgaggtggaggagtagtgctgaatt-tgacgagattctggatgtccttgcagCCTCTGTTCCCCGGAGAGAGTGGAGTGGATCAATTGGTGGAGATTATCAAG-
upper sequence: GLYMA18G45960.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S60_100V6.1 (Physcomitrella patens), 3'ss of exon 7
----aagataattccttcctggaagccactaattaggtcttattgaataaatgacacatttttagattgatgcttatctatgattatgttgtgc---tatttgcagcCAATGTTTCCCGGAGAGAGTGGGGTTGATCAATTGGTAGAGATCATTAAGG
| | | | || ||| | | | | | | ||| | | ||| || | |||| | | ||| | || || | |||||||| |||| |||||||||||||| || ||||||||||| ||||| ||||||
catgtgtgtgtatgcgtgttgcaagtcgg-agtcatggagt-ttgggtgagtgaggtggg---ggagtagtgctgaatt-tgacgagattttggatgtccttgcagCCTCTGTTCCCCGGAGAGAGTGGAGTAGATCAATTGGTGGAGATTATTAAG-Mapped 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|151396011|gb|EV265888.1|EV265888EST: TGATATTTGGTCTGCTGGTTGTGTGTTGGCTGAGCTTCTTGTAGGACATC CAATGTTTCCCGGAGAGAGTGGGGTTGATCAATTGGTAGAGATCATTAAGA
genomic: TGATATTTGGTCTGCTGGTTGTGTGTTGGCTGAGCTTCTTGTAGGACATGtgagaattta ... tatttgcagcCAATGTTTCCCGGAGAGAGTGGGGTTGATCAATTGGTAGAGATCATTAAGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatgacacatttttagattgatgcttatctatgattatgttgtgctatttgcagcCAATGTTTCCCGGAGAGAGTGGGGTTGATCAATTGGTAGAGATCATTAAGG
gattgat putative branch site (score: 4)
atttttagattgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aagataattccttcctggaagccactaattaggtcttattgaataaatgacacatttttagattgatgcttatctatgattatgttgtgctatttgcagcCAATGTTTCCCGGAGAGAGTGGGGTTGATCAATTGGTAGAGATCATTAAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - -ccttcct
- - - - - - - - - - -ccactaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgtg