Sequence
atgc intronic sequence ATGC exonic sequence...tcttttctcacactcctcttttattaattaagtcattgtttgattatcacatccctatttttgacattctcgattctgtttccttatcttctgaataaagGTATCTTGTTGTATGAGATGCTCTATGGTCGTACACCATTCAGAGGAAAGAATAGACAGAAGACATTTTCCAATATTTTACACAAGGATCTTACCTTTCC
Basic information
species | Glycine max |
transcript | GLYMA08G33520.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G33520.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os04g23890.3 (Oryza sativa), 3'ss of exon 19
tcttttctcacactcctcttttatta-attaagtcattgtttgattatcacatccctatttttgacattctcgattctgtttcctt--atcttctgaataaagGTATCTTGTTGTATGAGATGCTCTATGGTCGTACACCATTCAGAGGAAAGAATAGACAGAAGACATTTTCCAATATTTTACACAAGGATCTTACCTTTCC
||| | | ||| |||| |||||||||| || ||| | | | || || | | | | | || | || ||| || | |||||||||||||| ||||| |||||||| ||| |||||||||| || | |||||||||| || || | ||||| || ||||| |||||
-aaccatgagaacttgtttgatatggcattattatattgtttgatatgcattatgctaataataagatgac--atccagctaacatcaattcccatgctatagGAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGAACAGGAAAAAGACATTTTATAACATACTGCACAAAGACCTTACATTTCC
upper sequence: GLYMA08G33520.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G58140.2 (Arabidopsis thaliana), 3'ss of exon 20
tcttttctcacactcctcttttattaattaagtcattgtttgattatcacatccctatttttgacattctcgattctgtttccttatcttctgaataaagGTATCTTGTTGTATGAGATGCTCTATGGTCGTACACCATTCAGAGGAAAGAATAGACAGAAGACATTTTCCAATATTTTACACAAGGATCTTACCTTTCC
| | || | ||| ||| | ||| ||||| | | || || || | || ||| ||| || | | | | | |||||||||||||||||||||||| |||||||| ||||| ||||| || |||||||| || ||||||||| |||| || || ||||| ||||| || || ||
-------gtataatctgccactatct-ttaccttatt--ttgatcacaaa----ctgttattaatatgctca--tctccttttatgtgtgtttgttgtagGTATCTTGTTGTATGAGATGCTTTATGGTCGCACACCTTTCAGGGGTAAGAATAGGCAAAAGACATTTGCCAACATCTTGCACAAAGATCTCACTTTCCC
upper sequence: GLYMA08G33520.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv03s0038g04210.t01 (Vitis vinifera), 3'ss of exon 19
--tcttttctcacactcctcttttattaattaagtcattgtttgattatcacatccctatttttgacattctcgattctgtttccttatcttctgaataaagGTATCTTGTTGTATGAGATGCTCTATGGTCGTACACCATTCAGAGGAAAGAATAGACAGAAGACATTTTCCAATATTTTACACAAGGATCTTACCTTTCC
||||| | | || | | || | ||| | | || |||| | || | ||||| | | || | ||| || || ||||||||||||| ||||| ||||| || ||||||||||||||||| ||||||||||||||||| || || ||||| ||||| || |||||
aacctttttctgcttaatttgcttgctggaggatattctgcctaattcttctagtccccattttcatgccttca--tttgtttgttcctgtttgattttcagGGATTTTTCTGTATGAGATGCTTTATGGCCGTACTCCTTTCAGAGGAAAGAATAGGCAGAAGACATTTTCCAACATCTTGCACAAAGATCTGACTTTTCCMapped 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|46492935|gb|CN472491.1|CN472491EST: AATTATAACTGGAGCTGGGCATACTAGCGGTATAGATTGGTGGACCCTTG GTATCTTGTTGTATGAGATGCTCTATGGTCGTACACCATTCAGAGGAAAGA
genomic: AATTATAACTGGAGCTGGGCATACTAGCGGTATAGATTGGTGGACCCTTGgtaagcactt ... ctgaataaagGTATCTTGTTGTATGAGATGCTCTATGGTCGTACACCATTCAGAGGAAAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcacatccctatttttgacattctcgattctgtttccttatcttctgaataaagGTATCTTGTTGTATGAGATGCTCTATGGTCGTACACCATTCAGAGGAAAGAATAGACAGAAGACATTTTCCAATATTTTACACAAGGATCTTACCTTTCC
ttttgac putative branch site (score: 3)
ttctgtttccttatct putative PPT
tatttttga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcttttctcacactcctcttttattaattaagtcattgtttgattatcacatccctatttttgacattctcgattctgtttccttatcttctgaataaagGTATCTTGTTGTATGAGATGCTCTATGGTCGTACACCATTCAGAGGAAAGAATAGACAGAAGACATTTTCCAATATTTTACACAAGGATCTTACCTTTCC
- - - - - - ctcctct
- - - - - - - - - - - - - - - - - -ttgtttg
- - - - - - - - - - - - - - - - - - - - - - - -cacatcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cattctc