Sequence
atgc intronic sequence ATGC exonic sequence...gcttccaattttttaatccatatgattagcgtaacattcatagacaaatacatagtcaccacatatgggattaataattgctgtaaatgtttctatgtagGTGGTAGGAACTCCTAATTACATGTGCCCTGAACTGCTTGCTGATATTCCATATGGATTCAAATCTGATATTTGGTCACTAG
Basic information
species | Glycine max |
transcript | GLYMA12G09910.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G09910.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os01g64490.1 (Oryza sativa), 3'ss of exon 9
-gcttccaattttttaatccatatgatta-gcgtaacattcatagacaaatacatagtcaccacatatgggattaataattgctgtaaatgtttctatgtagGTGGTAGGAACTCCTAATTACATGTGCCCTGAACTGCTTGCTGATATTCCATATGGATTCAAATCTGATATTTGGTCACTAG
|| |||| | | ||||| | | | | || || || | | | | | | | | || | ||| | || ||||| || ||||| || |||||||||||||| || |||||||| || ||||| || |||||||| || || || ||||| || |
tatgtcgaattgatc--cctatatgttcaagtggaatatcattatgttagctaaatacctttatgttctcaaattcttatattttggcatgatgcttcttagGTTGTGGGAACACCAAATTACATGTGCCCAGAGCTGCTTGCAGACATTCCTTACGGATTCAAGTCAGACATATGGTCTCTTG
upper sequence: GLYMA12G09910.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G137118_T02 (Zea mays), 3'ss of exon 9
gcttccaattttttaatccatatgattagcgtaacattcatagacaaatacatagtcaccacatatgggattaataattgctgtaaatgt-ttctatgtagGTGGTAGGAACTCCTAATTACATGTGCCCTGAACTGCTTGCTGATATTCCATATGGATTCAAATCTGATATTTGGTCACTAG
| || | || | | | | | || || || || || || || | ||||| || || | | || | | |||||||| || || || |||||||||||||| || ||||| ||||||||||| ||||| ||||| || || || ||||| || |
atgaaccatgtagatatgctagtccatctcatggaatgtatggaagtgta-attgtgcttttgcattcgtgcaataactggtggcaccatgttttttttagGTGGTCGGGACACCAAATTACATGTGCCCAGAGCTGCTAGCTGATATTCCCTATGGTTTCAAGTCAGACATCTGGTCTCTCG
upper sequence: GLYMA12G09910.1 (Glycine max), 3'ss of exon 8
lower sequence: AT3G44200.1 (Arabidopsis thaliana), 3'ss of exon 8
gcttccaattttt-taatccatatgattagcgtaacattcatagacaaatacatagtc--accacatatgggattaataattgctgtaaatgtttctatgtagGTGGTAGGAACTCCTAATTACATGTGCCCTGAACTGCTTGCTGATATTCCATATGGATTCAAATCTGATATTTGGTCACTAG
||| || | || | || |||| | | | | || ||||| |||| | | |||| || || | | | | ||| ||| ||||| || |||||||| || ||||||||||| ||||||||||||||||| || ||||| || || || ||||| ||||| |||
-tccataatgattattattcttaggattgctctcaagcttctgaactaatacttagtgtgatagaaaatggtgtttatgact--catggaattttatatttagGTTGTTGGAACTCCAAACTACATGTGCCCGGAACTGCTTGCTGATATCCCTTATGGTTTTAAGTCAGATATCTGGTCCTTAG
upper sequence: GLYMA12G09910.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv06s0009g00690.t01 (Vitis vinifera), 3'ss of exon 8
gcttccaattttttaatccatatgattagcgtaacattcatagaca-aatacatagtcaccacatatgggattaa--taattgctgtaaatgtttctatgtagGTGGTAGGAACTCCTAATTACATGTGCCCTGAACTGCTTGCTGATATTCCATATGGATTCAAATCTGATATTTGGTCACTAG
| || | || | || | | | ||||| ||| || || | | | | || | | | | | | |||| || |||||||| ||||||||||| |||||||| ||||| |||||||| ||||| |||||||||||||| ||||| ||||
--gttgaaatcttgcctgtgcttgtcctgt-tgatattcacggacttggtaaatttgagcaatgggacacgctcacctattcatttcctacttatgtgcacagGTAGTTGGAACTCCCAATTACATGTGTCCTGAACTTCTTGCAGATATTCCTTATGGCTTCAAATCTGATATCTGGTCTCTAG
upper sequence: GLYMA12G09910.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S22_216V6.1 (Physcomitrella patens), 3'ss of exon 8
----------------------------------------------------gcttccaattttttaatccatatgattagcgtaacattcatagacaaatacatagtcaccacatatgggattaataattgctgtaaatgtttctat-gtagGTGGTAGGAACTCCTAATTACATGTGCCCTGAACTGCTTGCTGATATTCCATATGGATTCAAATCTGATATTTGGTCACTAG
||| ||| ||| |||| | |||| ||| | || | || ||| || | | ||||| | || |||| | |||| ||||| ||||| ||||||||||| || || || ||||| || || ||||||||||||||||| || ||||||||| |||
gtaagtaatccgttgtgaacctcgtatcatttgcattggaatgatgatcgctgctgtgaatagtttttaccatctcgcggtcgtactgttcgtttggaagt---taatcaatccactaatggccggaacgtgctgct--tcttgctattgcagGTAGTAGGCACTCCAAATTACATGTGTCCAGAGCTACTTGCAGACATCCCATATGGATTCAAATCAGACATTTGGTCATTAGMapped 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|5058284|gb|AI736760.1|AI736760EST: GGGATTTCGGGCTTGCTAAGACACTAAAAGCAGATGATTTGGCATCTTCG GTGGTAGGAACTCCTAATTACATGTGCCCTGAACTGCTTGCTGATATTCCA
genomic: GGGATTTCGGGCTTGCTAAGACACTAAAAGCAGATGATTTGGCATCTTCGgtatgtgtaa ... ttctatgtagGTGGTAGGAACTCCTAATTACATGTGCCCTGAACTGCTTGCTGATATTCCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaatacatagtcaccacatatgggattaataattgctgtaaatgtttctatgtagGTGGTAGGAACTCCTAATTACATGTGCCCTGAACTGCTTGCTGATATTCCATATGGATTCAAATCTGATATTTGGTCACTAG
gattaat putative branch site (score: 3)
tgtttct putative PPT
attaataatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcttccaattttttaatccatatgattagcgtaacattcatagacaaatacatagtcaccacatatgggattaataattgctgtaaatgtttctatgtagGTGGTAGGAACTCCTAATTACATGTGCCCTGAACTGCTTGCTGATATTCCATATGGATTCAAATCTGATATTTGGTCACTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
gcttcca
- - - - - - - - -ccatatg
- - - - - - - - - - - - - - - - -acattca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - caccaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgta