Sequence
atgc intronic sequence ATGC exonic sequence...actgtgtatttgtacactttcatgtcagtgcaacttatactccaatcgtttctttatttcttatatgtctatgctttctctatcgcttgttctcatgcagTCAGATGAACACTGTTGTAATTCTTGTGAAGAAGTGCGTGAAGCATATAGGAAAAAGGGCTGGGCAATGACAAATATGGATTTGATTGATCAG
Basic information
species | Glycine max |
transcript | GLYMA05G24610.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G24610.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g41120.1 (Oryza sativa), 3'ss of exon 5
-----------actgtgtatttgtacactttcatgtcagtgcaacttat-actccaatcgttt---ctttatttcttatatgtc-tatgctttctct--atcgcttgttctcatgcagTCAGATGAACACTGTTGTAATTCTTGTGAAGAAGTGCGTGAAGCATATAGGAAAAAGGGCTGGGCAATGACAAATATGGATTTGATTGATCAG
| | || | | | | | ||| | | ||||| | | || | | ||| || || | ||| || || ||| || |||| | | ||||| |||||||| || |||||||||||||||||||| | |||||||||| ||| || || ||||| | |||||| ||| ||||||| |||
gtatgcacaatcttttctaatgggaatgtattttgtttatacctcttattatttcagctttctgaacttaccttgttctttgttacattctaactccggatggctttctggacttcagTCGGATGAACAATGCTGTAATTCTTGTGAAGAAGTTAGGGAAGCATATAAGAAGAAAGGATGGGCCCTTACAAATCCTGATCTGATTGACCAG
upper sequence: GLYMA05G24610.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G044457_T01 (Zea mays), 3'ss of exon 5
----------------actgtgtatttgtacactttcatgtcagtgcaacttatactccaatcgtttctttatttcttatatgtctatgctt---tctctatcgcttgttctca---------tgcagTCAGATGAACACTGTTGTAATTCTTGTGAAGAAGTGCGTGAAGCATATAGGAAAAAGGGCTGGGCAATGACAAATATGGATTTGATTGATCAG
| | |||| | ||| | | | || ||||| || | ||| | | | | | |||| | | || | || |||| | | ||||| |||||||| |||||||||||||| |||||||| || || ||||||| ||| || || ||||| |||||||| || | ||||| |||
gtacgtgctccttttttttccctttttggttaattttgttttaatgtaacttttatttcaacattctttatccatgttatgctttacttctcaacttcgaattgcttcaacctacttggaaagctcagTCGGATGAACAATGTTGTAATTCTTGCGAAGAAGTCCGGGAGGCATATAAGAAGAAAGGATGGGCTCTGACAAATCCTGACCTAATTGACCAG
upper sequence: GLYMA05G24610.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv12s0178g00020.t01 (Vitis vinifera), 3'ss of exon 5
--actgtgtatttgtacactttcatgtcagtgcaacttatactcc-aatcgtttctttatttcttatatgtctatgctttctctatcgcttgttctcatgcagTCAGATGAACACTGTTGTAATTCTTGTGAAGAAGTGCGTGAAGCATATAGGAAAAAGGGCTGGGCAATGACAAATATGGATTTGATTGATCAG
| | | | ||| | | || | || || | | | | | ||||| || | | ||| | || | || | | ||| |||| | ||||| | ||||||||||| ||||| ||||| |||||||||||||| || || || |||| ||||||||| |||||||||||||||
ttagtatttgtttcatgatggatcttccaatacacaataaatttctgaatgcatctttgttctgt---tatctgtttgttttttaattcattctctttggcagACGGATGATGATTGTTGTAATTCATGTGATGAAGTTCGTGAAGCATATAGAAAGAAAGGTTGGGGGATGACAAATCCAGATTTGATTGATCAG
upper sequence: GLYMA05G24610.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S15_354V6.1 (Physcomitrella patens), 3'ss of exon 6
--actgtgtatttgtacactttcatg-tcagtgcaacttatactccaatcgtttctttatttcttatatgtctatgctttctctatcgcttgttctcatgcagTCAGATGAACACTGTTGTAATTCTTGTGAAGAAGTGCGTGAAGCATATAGGAAAAAGGGCTGGGCAATGACAAATATGGATTTGATTGATCAG
| | ||| | | | | ||| | | || | || | || | | || || | | | | | || || | ||||||||||| || || ||||| || |||||||| ||||| ||||||||| | |||||||| ||||| |||| |||| |||| | |||||||||
gtagcacgcattaggaaagaaatgggctcaatctgccctacatgaaaaagctctcatagatctaaatctg---acacatggtgggatgtgtggactgctccagTCAGATGATCAATGCTGTAACTCATGTGAAGAGGTGCGAGAAGCATATCGCAAAAAGGGTTGGGCCTTGACCAATACGGATCTAATTGATCAGMapped 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|193441507|gb|FK405078.1|FK405078EST: GACTTGGACATGATGAAAAGTATTGTGGTTCATGTTTTGGTGCAGAAGAG TCAGATGAACACTGTTGTAATTCTTGCGAAGAAGTGCGTGAAGCATATAGG
genomic: GACTTGGACATGATGAAAAGTATTGTGGTTCATGTTTTGGTGCAGAAGAGgtacctttga ... tctcatgcagTCAGATGAACACTGTTGTAATTCTTGTGAAGAAGTGCGTGAAGCATATAGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcgtttctttatttcttatatgtctatgctttctctatcgcttgttctcatgcagTCAGATGAACACTGTTGTAATTCTTGTGAAGAAGTGCGTGAAGCATATAGGAAAAAGGGCTGGGCAATGACAAATATGGATTTGATTGATCAG
ctttctctatcgcttg CT-rich tract
tctttatttcttatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
actgtgtatttgtacactttcatgtcagtgcaacttatactccaatcgtttctttatttcttatatgtctatgctttctctatcgcttgttctcatgcagTCAGATGAACACTGTTGTAATTCTTGTGAAGAAGTGCGTGAAGCATATAGGAAAAAGGGCTGGGCAATGACAAATATGGATTTGATTGATCAG
-ctgtgta
- - - - - tgtacac
- - - - - - - - - -tcatgtc
- - - - - - - - - - - - - - tgcaact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctatgct