Sequence
atgc intronic sequence ATGC exonic sequence...tgtgtatttgtacactttcatgtcagtgcaacttatactctccaatcgtttcttaatttcttatacgtctatgctttttctctcactcgttctcatgcagTCAGATGAACACTGTTGTAATTCTTGCGAAGAAGTGCGTGAAGCATATAGGAAAAAAGGCTGGGCAATGACAAATATGGATTTGATTGATCAG
Basic information
species | Glycine max |
transcript | GLYMA08G07840.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G07840.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g41120.1 (Oryza sativa), 3'ss of exon 5
-------------tgtgtatttgtacactttcatgtcagtgcaacttatactctccaatcgtt--tcttaatttcttatacgtctatgctttttctctcactcgttctcatg----cagTCAGATGAACACTGTTGTAATTCTTGCGAAGAAGTGCGTGAAGCATATAGGAAAAAAGGCTGGGCAATGACAAATATGGATTTGATTGATCAG
| | || | | | | | ||| | | ||||| | || | | |||| || || | || || | | ||| | | | || | ||||| |||||||| || ||||||||||| |||||||| | |||||||||| ||| ||||| ||||| | |||||| ||| ||||||| |||
gtatgcacaatcttttctaatgggaatgtattttgtttatacctcttattatttcagctttctgaacttaccttgttctttgt-tacattctaactccggatggctttctggacttcagTCGGATGAACAATGCTGTAATTCTTGTGAAGAAGTTAGGGAAGCATATAAGAAGAAAGGATGGGCCCTTACAAATCCTGATCTGATTGACCAG
upper sequence: GLYMA08G07840.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G044457_T01 (Zea mays), 3'ss of exon 5
------------------tgtgtatttgtacactttcatgtcagtgcaacttatactctccaatcgtttcttaatttc---ttatacgtctatgctt----tttctctcactcgttctca---tgcagTCAGATGAACACTGTTGTAATTCTTGCGAAGAAGTGCGTGAAGCATATAGGAAAAAAGGCTGGGCAATGACAAATATGGATTTGATTGATCAG
| | |||| | ||| | | | || ||||| || | || ||| | || | | ||| ||| ||| || || || | | ||||| |||||||| ||||||||||||||||||||||| || || ||||||| ||| ||||| ||||| |||||||| || | ||||| |||
gtacgtgctccttttttttccctttttggttaattttgttttaatgtaacttttatttcaacattctttatccatgttatgctttacttctcaacttcgaattgcttcaacctacttggaaagctcagTCGGATGAACAATGTTGTAATTCTTGCGAAGAAGTCCGGGAGGCATATAAGAAGAAAGGATGGGCTCTGACAAATCCTGACCTAATTGACCAG
upper sequence: GLYMA08G07840.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G161019_T01 (Zea mays), 3'ss of exon 5
-tgtgtatttgtacactttcatgtcagtgcaacttatactctccaa----tcgtttcttaatttcttatacgt-ctatgctttttctctcactcgttctca-tgcagTCAGATGAACACTGTTGTAATTCTTGCGAAGAAGTGCGTGAAGCATATAGGAAAAAAGGCTGGGCAATGACAAATATGGATTTGATTGATCAG
| || | | |||| | | || || || | | | | | |||| ||| ||||| | | |||||||| || || ||| | ||||| ||||| || || |||||||||||||||||||| | |||||||||| ||| ||||| ||||| | |||||| || | ||||| |||
gtatgcacaccttt-ttttctttttggttcattttgttttattataacttttatttcagcattccttatccatgttatgctttg-cttggacctactctgagctcagTCGGATGAGCAATGCTGTAATTCTTGCGAAGAAGTCAGGGAAGCATATAAGAAGAAAGGGTGGGCTCTAACAAATCCTGACCTAATTGACCAG
upper sequence: GLYMA08G07840.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv12s0178g00020.t01 (Vitis vinifera), 3'ss of exon 5
----tgtgtatttgtacactttcatgtcagtgcaacttatactctccaatcgtttcttaatttcttatacgtctatgctttttctctcactcgttctcatgcagTCAGATGAACACTGTTGTAATTCTTGCGAAGAAGTGCGTGAAGCATATAGGAAAAAAGGCTGGGCAATGACAAATATGGATTTGATTGATCAG
| | | ||| | | || | || || | | ||| | || | | |||| || | | ||||| ||| || ||| |||| | ||||| | ||||||||||| || || ||||| |||||||||||||| || ||||| |||| ||||||||| |||||||||||||||
ttagtatttgtttcatgatggatcttccaatacacaataaatttctgaatgcatctttgttctgttatctgtttgt--tttttaattcattc--tctttggcagACGGATGATGATTGTTGTAATTCATGTGATGAAGTTCGTGAAGCATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAGMapped 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|192326043|gb|FK016915.1|FK016915EST: GACTTGGACATGATGAAAAGTATTGTGGTTCATGTTTTGGTGCAGAAGAG TCAGATGAACACTGTTGTAATTCTTGCGAAGAAGTGCGTGAAGCATATAGG
genomic: GACTTGGACATGATGAAAAGTATTGTGGTTCATGTTTTGGTGCAGAAGAGgtaccttcga ... tctcatgcagTCAGATGAACACTGTTGTAATTCTTGCGAAGAAGTGCGTGAAGCATATAGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcgtttcttaatttcttatacgtctatgctttttctctcactcgttctcatgcagTCAGATGAACACTGTTGTAATTCTTGCGAAGAAGTGCGTGAAGCATATAGGAAAAAAGGCTGGGCAATGACAAATATGGATTTGATTGATCAG
ctctcac putative branch site (score: 3)
tctatgctttttctct CT-rich tract
tcttaatttcttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtgtatttgtacactttcatgtcagtgcaacttatactctccaatcgtttcttaatttcttatacgtctatgctttttctctcactcgttctcatgcagTCAGATGAACACTGTTGTAATTCTTGCGAAGAAGTGCGTGAAGCATATAGGAAAAAAGGCTGGGCAATGACAAATATGGATTTGATTGATCAG
- - - - tgtacac
- - - - - - - - -tcatgtc
- - - - - - - - - - - - - tgcaact
- - - - - - - - - - - - - - - - - - -ctctcca