Sequence
atgc intronic sequence ATGC exonic sequence...ttcatgctttgtgtgtggattatctttatgttttttttttctgcatcaagtccttttaacttcttaattgtgacttagttcaacttctgatgatctatagAGAATGTGGTGAGATGTGTGCAATGAAGGAGGTAACCCTTTTTTCTGATGATGCTAAATCAAGGGAAAGTGCGCAGCAACTTGGCCAA
Basic information
species | Glycine max |
transcript | GLYMA08G01880.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G01880.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g44642.1 (Oryza sativa), 3'ss of exon 3
ttcatgctttgtgtgtggattatctttatgttttttttttctgcatcaagtccttttaacttcttaattgtgacttagttcaacttctgatgatctata---gAGAATGTGGTGAGATGTGTGCAATGAAGGAGGTAACCCTTTTTTCTGATGATGCTAAATCAAGGGAAAGTGCGCAGCAACTTGGCCAA
|| ||||| || | || | |||| || |||| | || | || | || | ||| || | || | | || | || | || ||||| |||||||||||||||||||| |||||||| || || ||| ||||||||| |||||||| |||| | | ||
--tatcctttgagtagtgtgccactgactattttattaggactgatcat-cctttgtttctcttcaaatttgatataatataattctctgtcatttgtatcagTGATAAAGGTGAAATGTGTGCAATGAAGGAGGTCACCCTTTTCTCAGACGATCCTAAATCAAAAGAAAGTGCAAAGCAGTTGTGTCAG
upper sequence: GLYMA08G01880.1 (Glycine max), 3'ss of exon 2
lower sequence: AC209208.3_FGT001 (Zea mays), 3'ss of exon 2
-----ttcatgctt---tgtgtgtggattatctttatgttttttttttctgcatcaagtccttttaacttcttaattgtgacttagttcaacttctgatgatctatagAGAATGTGGTGAGATGTGTGCAATGAAGGAGGTAACCCTTTTTTCTGATGATGCTAAATCAAGGGAAAGTGCGCAGCAACTTGGCCAA
| | || | ||| | || || || ||||||| || || ||| | || ||| | ||| ||| || ||||| || | || | || || | ||||| |||||||| ||||||||||| |||||||| || |||||| ||||||||| |||||||| | || || ||||
ataactctaaactatcatctgtcttgactagctaaatgttttattgcacttggtca----ttatttgtttccttatt-tgaatt-gttca--ttatcatctatttcagTGACAGAGGTGAAATGTGTGCGATGAAGGAGGTTACCCTTTTCTCAGATGATCCTAAATCAAAAGAAAGTGCAAAACAGCTCTGCCAG
upper sequence: GLYMA08G01880.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G093316_T01 (Zea mays), 3'ss of exon 3
ttcatgctttgtgtgtggattatctttatgttttttttttctgcat-caagtccttttaacttcttaattgtgacttagttcaact---tctgatgatctat---agAGAATGTGGTGAGATGTGTGCAATGAAGGAGGTAACCCTTTTTTCTGATGATGCTAAATCAAGGGAAAGTGCGCAGCAACTTGGCCAA
| | | |||| | | | || | |||| ||| || | | || | | | || || || | | | | |||||| || || ||||| |||||||| ||||||||||| || ||||| || |||||| ||||||||| |||||||| | || || ||||
----taatcta---acggatcaggagtctcgcttgtacgcttgcacgtaaggccccattgcacagtagtcatcgcctattttaattgtttattgtcatctatttcagTGACAAAGGTGAAATGTGTGCGATGAAGGAGGTTACTCTTTTCTCAGATGATCCTAAATCAAAAGAAAGTGCAAAACAGCTGTGCCAG
upper sequence: GLYMA08G01880.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0025g03850.t01 (Vitis vinifera), 3'ss of exon 1
ttcatgctt-tgtgtgtggattatctttatgttttttttttctgcatcaagtccttttaacttcttaattgtgacttagttcaa--cttctgat-gatctatagAGAATGTGGTGAGATGTGTGCAATGAAGGAGGTAACCCTTTTTTCTGATGATGCTAAATCAAGGGAAAGTGCGCAGCAACTTGGCCAA
||||| | ||| ||| |||| | | | | | | ||| | | || ||| ||||| |||||| || ||| || | | || ||| ||| |||| ||||||||||||||||||||||| || | ||||| |||||||| || |||| ||||||||| ||||| || ||||||
-gattgcttgcatttgtctatttaatttaagcaatctgctatttc-tcatgcattatt--ctttataattctgactttttttttttcttttgcttggactttagTGAAAGTGGGGAGATGTGTGCAATGAAGGAGGTTACATTATTTTCAGATGATGCGAAGTCAAAGGAAAGTGCACAGCAGCTGGGCCAA
upper sequence: GLYMA08G01880.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0025g03370.t01 (Vitis vinifera), 3'ss of exon 4
---ttcatgctt-tgtgtgtggattatctttatgttttttttttctgcatcaagtccttttaacttcttaattgtgacttagttcaacttctgat-gatctatagAGAATGTGGTGAGATGTGTGCAATGAAGGAGGTAACCCTTTTTTCTGATGATGCTAAATCAAGGGAAAGTGCGCAGCAACTTGGCCAA
| ||||| | ||| ||| |||| | | | | | | ||| | | || ||| || | |||||| || ||| || | | || ||| ||| |||| ||||||||||||||||||||||| || | ||||| |||||||| || |||| ||||||||| ||||| || ||||||
cagtgattgcttgcatttgtctatttagtttaagcaatctgctatttc-tcatgcattatt--ctttatatatctgactt--tttttcttttgcttggactttagTGAAAGTGGGGAGATGTGTGCAATGAAGGAGGTTACATTATTTTCAGATGATGCGAAGTCAAAGGAAAGTGCACAGCAGCTGGGCCAAMapped 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|9899677|gb|BE608645.1|BE608645EST: CAGTTGCTTGGAAGGGGAACATTTGGACATGTATATCTTGGTTTTAACAG AGAATGTGGTGAGATGTGTGCAATGAAGGAGGTAACCCTTTTTTCTGATGA
genomic: CAGTTGCTTGGAAGGGGAACATTTGGACATGTATATCTTGGTTTTAACAGgtctgtatca ... tgatctatagAGAATGTGGTGAGATGTGTGCAATGAAGGAGGTAACCCTTTTTTCTGATGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaagtccttttaacttcttaattgtgacttagttcaacttctgatgatctatagAGAATGTGGTGAGATGTGTGCAATGAAGGAGGTAACCCTTTTTTCTGATGATGCTAAATCAAGGGAAAGTGCGCAGCAACTTGGCCAA
ttttaacttcttaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttcatgctttgtgtgtggattatctttatgttttttttttctgcatcaagtccttttaacttcttaattgtgacttagttcaacttctgatgatctatagAGAATGTGGTGAGATGTGTGCAATGAAGGAGGTAACCCTTTTTTCTGATGATGCTAAATCAAGGGAAAGTGCGCAGCAACTTGGCCAA
-tcatgct
- - - - - gtgtgtg
- - - - - - - - - - - - - - - - - - - - ctgcatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgactt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acttctg