Sequence
atgc intronic sequence ATGC exonic sequence...caatggcttcaatttcttggtttagcaatattgtagtagtaatggccaaagtgaaaaatgaagtttgatagctgaataagggtgaatgataatattgcagGAGCTACTACAGGTGCACAACACAGAAGTGCACAGTGAAGAAACGCGTGGAGAGGTCATTTCAGGACCCAACCACTGTGATAACAACGTATGAAGGTCAG
Basic information
species | Glycine max |
transcript | GLYMA05G25770.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G25770.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g47560.1 (Oryza sativa), 3'ss of exon 4
--------------------------------------------caatg-gcttcaatttcttggtttagcaata-ttgtagtagtaatg---gc-caaagtgaaaaatgaagtttg--atag-ctga-ataagggtgaatgataatattgcagGAGCTACTACAGGTGCACAACACAGAAGTGCACAGTGAAGAAACGCGTGGAGAGGTCATTTCAGGACCCAACCACTGTGATAACAACGTATGAAGGTCAG
| || || | | | | ||| || ||| | | | || | | || || | ||| || |||| ||| | | |||| | |||||||||||||||||||||||| || ||||||||| | |||||||| || |||||| |||| | |||||||| | ||||| || ||||| || || ||
gtacgtatgtacagttacacacacgtatagtacgtgactcgtagctgtgcgcgtgtacgtgtaccggccgcagtagttgcaccggacgcgcgcgcgcgcggcagaatgcgatgattgcaatgatctgatatatacggggttgatttttttgcagGAGCTACTACAGGTGCACGACGCAGAAGTGCCCGGTGAAGAAGCGGGTGGAGCGGTCGTACCAGGACCCGGCGGTGGTGATCACCACGTACGAGGGCAAG
upper sequence: GLYMA05G25770.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os05g49100.1 (Oryza sativa), 3'ss of exon 2
-------caatggcttcaatttcttggtttagcaatat-tgtagtagtaatggccaaagtgaaaaatgaagtttgatagctgaataagggtgaatgataatattgcagGAGCTACTACAGGTGCACAACACAGAAGTGCACAGTGAAGAAACGCGTGGAGAGGTCATTTCAGGACCCAACCACTGTGATAACAACGTATGAAGGTCAG
||| | || ||| | | | || |||| || | | | || | | | | ||||| | || || || || ||| ||||||||||||||| ||||||| || ||||||||| | |||||||| | |||||| |||| | |||||| | | ||||| || || || || || ||
ttatgaatcatgaatgca-tttggtagctgagatatatatggatcattgataattgattagggttcttacgtttgtgtgatggat--ggatggatggg-----tgcagGAGCTACTACCGGTGCACGACGCAGAAGTGCCCGGTGAAGAAGAGGGTGGAGCGGTCGTACCAGGACGCGGCGGTGGTGATCACCACCTACGAGGGGAAG
upper sequence: GLYMA05G25770.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g43650.1 (Oryza sativa), 3'ss of exon 2
-----------------------------------------------------------------caatggcttcaatttcttggtttagcaatattgtagtagtaatg-gccaaagtgaaaaatgaagtttgatagctgaataagggtgaatgataatattgcagGAGCTACTACAGGTGCACAACACAGAAGTGCACAGTGAAGAAACGCGTGGAGAGGTCATTTCAGGACCCAACCACTGTGATAACAACGTATGAAGGTCAG
| | || || | |||| | | | | | | |||| | || || | | | | | |||| |||||||||||||||||||| ||||||| || | |||||| |||||||| || |||||| |||| | |||||||| |||| ||||| || ||||| ||||| |||
gtacacatctatatacatgtacaaaccttaatttcacccagttgttgtagcacatacatatatcgtagtataccatgttactgtgccatacaattgcatggcacgatggtgttcaagt---actccaatttcaaaatgcaattcaattcgaattcgaatattgcagGAGCTACTACCGGTGCACGACGCCCAAGTGCGGTGTGAAGAAGCGGGTGGAGCGGTCGTACCAGGACCCCTCCACGGTGATCACCACGTACGAAGGGCAG
upper sequence: GLYMA05G25770.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G151763_T01 (Zea mays), 3'ss of exon 2
--caatggcttcaatttcttggtttagcaatattgtagtagtaatggccaaagtgaaaaatgaagtttgatagctgaataagggtgaatgataatattgcagGAGCTACTACAGGTGCACAACACAGAAGTGCACAGTGAAGAAACGCGTGGAGAGGTCATTTCAGGACCCAACCACTGTGATAACAACGTATGAAGGTCAG
|| | | || | | | | |||| | | | | || | | | | || | | | | | | | | | |||||||||||||| ||||||| || ||||||||| | |||||||| || |||||| |||| | |||||||| | ||||| || ||||| || || ||
cgcacagtgtccatgatgtagctatagctagac-atgctgcgtttgcgtgagctaatggtgggagcgctgcgaccgtgatggcgcgtacgtgtacgt-gcagGAGCTACTACCGGTGCACGACGCAGAAGTGCCCCGTGAAGAAGCGGGTGGAGCGGTCGTCCCAGGACCCGGCGGTGGTGATCACCACGTACGAGGGCAAG
upper sequence: GLYMA05G25770.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G453571_T01 (Zea mays), 3'ss of exon 2
caatggcttca-atttcttggtttagcaatattgtagtagtaatggccaaagtgaaaaatgaagtttgatagctgaataagggtgaatgataatattgcagGAGCTACTACAGGTGCACAACACAGAAGTGCACAGTGAAGAAACGCGTGGAGAGGTCATTTCAGGACCCAACCACTGTGATAACAACGTATGAAGGTCAG
| | || | | | |||| | || | || ||| | | | ||| || | ||| || |||||||||||||| ||||||| || ||||||||| | |||||||| || |||||| |||| | |||||| | | ||||| || ||||| || || ||
tagggttcccacacgacacgagcgagcagcaatgagcatatggtgaccacgtcgtactgactgatacaataatgcaacgata-tgatgcatgggcgcgcagGAGCTACTACCGGTGCACGACGCAGAAGTGCCCGGTGAAGAAGCGGGTGGAGCGGTCGTACCAGGACGCGGCGGTGGTGATCACCACGTACGAGGGCAAG
upper sequence: GLYMA05G25770.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM5G812272_T02 (Zea mays), 3'ss of exon 2
---------------------------------------caatggcttcaatttcttggtttagcaatattgtagtagtaatggccaaagtgaaaaatgaagtttg-atagctgaataagggtgaatgataatat--tgcagGAGCTACTACAGGTGCACAACACAGAAGTGCACAGTGAAGAAACGCGTGGAGAGGTCATTTCAGGACCCAACCACTGTGATAACAACGTATGAAGGTCAG
| ||||| | | | |||| | | | ||| | | | || || |||| || || |||| | || ||||||||||||||| ||||||| || |||| |||| | |||||||| || |||||| |||| |||||||| | ||||| || ||||| ||||| ||
gtacgtggtacatgcacagcacgtatatacagctatacctactggctactgcacgtatatacagcacctctcttcgatcctactccatgacgtacggtacggtagacattgctgcatgag--ctaatggtgatggcgtgcagGAGCTACTACCGGTGCACGACGCAGAGGTGCCCCGTGAAGAAGCGGGTGGAGCGGTCGCACCAGGACCCGGCGGTGGTGATCACCACGTACGAAGGCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccaaagtgaaaaatgaagtttgatagctgaataagggtgaatgataatattgcagGAGCTACTACAGGTGCACAACACAGAAGTGCACAGTGAAGAAACGCGTGGAGAGGTCATTTCAGGACCCAACCACTGTGATAACAACGTATGAAGGTCAG
gtttgat putative branch site (score: 5)
tgaatgataatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caatggcttcaatttcttggtttagcaatattgtagtagtaatggccaaagtgaaaaatgaagtttgatagctgaataagggtgaatgataatattgcagGAGCTACTACAGGTGCACAACACAGAAGTGCACAGTGAAGAAACGCGTGGAGAGGTCATTTCAGGACCCAACCACTGTGATAACAACGTATGAAGGTCAG
- -tggcttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - aatgaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gggtgaa