Sequence
atgc intronic sequence ATGC exonic sequence...gtggatggattatggattggaacttcaaacttctgcttatactctttgttttgattatatccattgtatgttctcatgtaaaagattatatgttttgtagGGTCCCTGCCTCTTCCATGGTCCATTAGGATGAAAATTGCACTTGGAGCTGCAAAGGGTCTTGCTTTTCTTCATGAGGAAGCTGAACGACCAGTAATATA
Basic information
species | Glycine max |
transcript | GLYMA08G40770.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G40770.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 3
---------------------------------------------------------------------------gtggatggattatggattggaacttc--aaacttctgcttat-actctttgtt--ttgattatatccattgtatgttctcatgtaaaagattatatgttttgt-----------agGGTCCCTGCCTCTTCCATGGTCCATTAGGATGAAAATTGCACTTGGAGCTGCAAAGGGTCTTGCTTTTCTTCATGAGGAAGCTGAACGACCAGTAATATA
|| || | || | | |||| || | || | || | ||| | | || | || || | || | || ||||||| ||| | |||||| || ||||| || |||||||| || ||||| |||| |||||||| ||||||||||||||||| |||||||| ||||| ||| ||||||| || ||
gtacgtgtctgaccagtttctcaagacattgaaacttcaatttgtatacaatgcctgtgctttaatgaatgaacttatcattcatatttgagtagctcttctgaagtgtttggtcattgcatcttgctgctggaaaaaatattaaatagatagaaatattgaatcttatatgatttatgattcacctatagGGTCTCTTCCTCTCCCTTGGTCCATCAGAATGAAGGTTGCTCTTGGAGCAGCAAAGGGTCTTGCTTTCCTTCATGAAGAAGCAGAAAGACCAGTTATTTA
upper sequence: GLYMA08G40770.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g40590.1 (Oryza sativa), 3'ss of exon 3
-gtggatggattatggattggaacttcaaact---tctgcttatactctttgttttgattatatccattgtatgttctcatgtaaaagattatatgttttgtagGGTCCCTGCCTCTTCCATGGTCCATTAGGATGAAAATTGCACTTGGAGCTGCAAAGGGTCTTGCTTTTCTTCATGAGGAAGCTGAACGACCAGTAATATA
|| | | | ||| || | | | | | || ||| | | || ||| || || || | | | ||| ||| | |||||| | ||||| |||||| |||| || |||| ||| |||||||| ||||| ||||| ||||||||||||||||| ||||||||| | ||||| || ||
gttgcgttaaatttggcccaactgtttcatttcagtataactctattctgaagtgtc-ttgtatttatctgatatttgtct-tggataattgtat--taaacagGGTCTTTACCTCTCCCATGGGCCATCAGAATGAGAATAGCACTTGGTGCTGCTAAGGGCCTTGCTTTTCTTCATGAAGAAGCTGAAAGGCCAGTTATCTA
upper sequence: GLYMA08G40770.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G028037_T02 (Zea mays), 3'ss of exon 3
gtggatggattatggattggaacttcaaacttctgcttatactctttgttttgattatatccattgtatgttc-tcatgtaaaagattatatgtttt--gtagGGTCCCTGCCTCTTCCATGGTCCATTAGGATGAAAATTGCACTTGGAGCTGCAAAGGGTCTTGCTTTTCTTCATGAGGAAGCTGAACGACCAGTAATATA
|||| ||||| | | | | | || || | | | | | || | || | || ||| | || | ||| | ||| ||| ||||||| |||||| ||||||| ||||||||||| ||||| ||||| || || || |||||||||||||| ||||||||| |||||||||| ||
-aggatt--ttatgtgctaaatttgaccagtgttgttttgttttgtcataacatcttgaaccttcacatacccatctaataacattttttttgtatcaaatagAGTCATTGCCTCTACCATGGGCCATTAGAATGAAAATTGCTCTTGGTGCTGCGAAAGGCCTCGCTTTTCTTCATGAAGAAGCTGAAAGACCAGTAATCTA
upper sequence: GLYMA08G40770.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G132184_T03 (Zea mays), 3'ss of exon 3
--------------------------------------------------------------------------------------------gtggatggattatggattggaacttcaaacttctgcttatactctttgttttgattatatccat-----tgtatgttctcatgtaaaagattatatgtttt---gtagGGTCCCTGCCTCTTCCATGGTCCATTAGGATGAAAATTGCACTTGGAGCTGCAAAGGGTCTTGCTTTTCTTCATGAGGAAGCTGAACGACCAGTAATATA
| || || ||| | | | | | | || || | | ||||| || ||| ||| ||| | | ||| ||| | || | |||||||| || ||||| |||||| | || || ||||| ||||||| ||||| ||||||||||| ||||| |||||||| ||||| ||| ||||||| || ||
gtatgtatctagcttattccttagcgattggagcattaacttctctttaggattcaccttttattccttaagcaaataatcgtgtatcatatgagggtgcattgttgctctgctatatttatttgtgtagcttagacgggctttgaatagtatcatggaaatgttgaatcttaagcaaatcattgtgctttctgctgtagGGTCTCTTCCTCTCCCATGGGCAATCAGAATGAAGGTTGCACTCGGAGCAGCAAAGGGTCTGGCTTTCCTTCATGAAGAAGCAGAAAGACCAGTCATTTA
upper sequence: GLYMA08G40770.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G150806_T01 (Zea mays), 3'ss of exon 3
-------------------------------------------------------------------------------------------gtggatggattatggatt--ggaacttcaaacttctgctta--tactctttgttttg-attatatccattgtatgttctcatgtaaaagattatatgtttt---gtagGGTCCCTGCCTCTTCCATGGTCCATTAGGATGAAAATTGCACTTGGAGCTGCAAAGGGTCTTGCTTTTCTTCATGAGGAAGCTGAACGACCAGTAATATA
| || | || ||| | | | || | ||||| | |||| | | || || || | | | | ||||| ||| | || | |||||||| || ||||| |||||| | || || ||||| ||||||| ||||| ||||||||||| ||||| |||||||| ||||| ||| | ||||| || ||
gtatgtatctggcttattccttaatgattggagcactaacttctgtttaggattcacctttttttcttaagcaaataatcgtgtatcatatgagggcgcatgatgttctcctgtatttatttgtgtagcttaggcatcctttaaatagtatcatggaaatgttgaatcttaaagtaaacaattctgctttctactgtagGGTCTCTTCCTCTCCCATGGGCTATCAGAATGAAGGTTGCACTGGGAGCAGCAAAGGGTCTGGCTTTCCTTCATGAAGAAGCAGAAAGTCCAGTCATTTA
upper sequence: GLYMA08G40770.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv01s0026g01620.t01 (Vitis vinifera), 3'ss of exon 3
gtggatggattatggattggaacttcaaacttctgcttatactctttgttttgattatatccattgt--atgttctcatgtaaaagattatatgttttgtagGGTCCCTGCCTCTTCCATGGTCCATTAGGATGAAAATTGCACTTGGAGCTGCAAAGGGTCTTGCTTTTCTTCATGAGGAAGCTGAACGACCAGTAATATA
||| | | || ||| ||| | ||| | || | ||||| ||||| ||| | ||||| || | | | | || | | ||||||| ||||||||||||||||| |||| ||||||||||||||||| || ||||| ||||||||||| ||||||||||||||||| ||| | ||||| |||||
atggttt-actagagatactgactccctgctttttgataaatgatttgtgagtgcaatatcaattattaatgttttctcatgata-acaattttatatgtagGGGCCCTGCCTCTTCCATGGGCCATAAGGATGAAAATTGCACTAGGTGCTGCTAAGGGTCTTGCATTTCTTCATGAGGAAGCAGAAAGGCCAGTTATATAMapped 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|17518732|gb|BM187774.1|BM187774EST: AGTATATGAATTTATGCCACGGGGAAGCCTGGAAAATCACTTGTTTAGGA GGTCCCTGCCTCTTCCATGGTCCATTAGGATGAAAATTGCACTTGGAGCTG
genomic: AGTATATGAATTTATGCCACGGGGAAGCCTGGAAAATCACTTGTTTAGGAgtaagttact ... tgttttgtagGGTCCCTGCCTCTTCCATGGTCCATTAGGATGAAAATTGCACTTGGAGCTG
EST:
gi|21889037|gb|BQ742250.1|BQ742250EST: AGTATATGAATTTATGCCACGGGGAAGCCTGGAAAATCACTTGTTTAGGA GGTCCCTGCCTCTTCCATGGTCCATTAGGATGAAAATTGCACTTGGAGCT
genomic: AGTATATGAATTTATGCCACGGGGAAGCCTGGAAAATCACTTGTTTAGGAgtaagttact ... tgttttgtagGGTCCCTGCCTCTTCCATGGTCCATTAGGATGAAAATTGCACTTGGAGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgttttgattatatccattgtatgttctcatgtaaaagattatatgttttgtagGGTCCCTGCCTCTTCCATGGTCCATTAGGATGAAAATTGCACTTGGAGCTGCAAAGGGTCTTGCTTTTCTTCATGAGGAAGCTGAACGACCAGTAATATA
ttttgat putative branch site (score: 4)
atgtaaaagattatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtggatggattatggattggaacttcaaacttctgcttatactctttgttttgattatatccattgtatgttctcatgtaaaagattatatgttttgtagGGTCCCTGCCTCTTCCATGGTCCATTAGGATGAAAATTGCACTTGGAGCTGCAAAGGGTCTTGCTTTTCTTCATGAGGAAGCTGAACGACCAGTAATATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
-tggatgg
- - - - - - - - - - - - - - -cttctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgtaa