Sequence
atgc intronic sequence ATGC exonic sequence...taactttgccttctgttgcatggtcttagtcatttagctctgtttccagctagtgaatgaaagtggactaacatgcattctcaattttttgtccatacagAAGCGTGATGATGCTCGACAGTTTATGAAGTTTCTTCATCCTGATCTTGGCGTTG
Basic information
species | Glycine max |
transcript | GLYMA10G41430.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G41430.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g02890.1 (Oryza sativa), 3'ss of exon 4
taactttgccttctgttgcatggtcttagtcatttagctctgtttccagctagtgaa---tgaaagtggactaacatgcattctcaatttt--ttgtccatacagAAGCGTGATGATGCTCGACAGTTTATGAAGTTTCTTCATCCTGATCTTGGCGTTG
| || || ||| | | || || | || || | || || | | | | || ||| ||| || || | | |||| |||||||||||| | || |||||||||| |||||| ||||||||||| ||||
-----gagaattgtgcatcattggtcttgttataaatatcataaaagagagaacaaaacctgtagtttgcatgggattcatactctgttccacttaatcttgcagACCCGTGATGATGCTAGGCAATTTATGAAGTATCTTCACCCTGATCTTGGTGTTG
upper sequence: GLYMA10G41430.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G095757_T02 (Zea mays), 3'ss of exon 4
-taactttgccttctgttgcatggtcttagtcatttagctct---gtttccagctagtgaatgaaagtggactaacatgcattctcaattttttgtccatacagAAGCGTGATGATGCTCGACAGTTTATGAAGTTTCTTCATCCTGATCTTGGCGTTG
| |||| || | | |||| | | | | ||| | || | || | ||| ||| | || | |||| |||||||||||| | || || ||||||| |||||||||||||||||| || |
acagtattgcagcaagtca---gagttcagtcgcaagattttaaagagtagagcaggaaaactta-gtatggcatttcatattttcattaactttgttttgcagACTCGTGATGATGCTAGGCAATTCATGAAGTATCTTCATCCTGATCTTGGTGTCG
upper sequence: GLYMA10G41430.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G110834_T02 (Zea mays), 3'ss of exon 4
-------taactttgccttctgttgcatggtcttagtcatttagctctgtttccagctagtgaatgaaagtggactaacatgcattctcaattttttgtccatacagAAGCGTGATGATGCTCGACAGTTTATGAAGTTTCTTCATCCTGATCTTGGCGTTG
|| | | |||| | ||| | || || | | || || | | | || | ||| ||| | ||| | | |||| |||||||||||| | || || ||||||| |||||||||||||||||| || |
atttcagcaagtcagacttcaatggcaaagattttaaagagaagagcgg----caaaatgt-agtcattatgtcatttcatattttcatgaactttgttt--tgcagACTCGTGATGATGCTAGGCAATTCATGAAGTATCTTCATCCTGATCTTGGTGTCG
upper sequence: GLYMA10G41430.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv01s0011g04370.t01 (Vitis vinifera), 3'ss of exon 5
--taactttgccttctgttgcatggtcttagtcatttagctctgtttccagctagtgaatgaaagtgg-actaacatgcattctcaattttttgtccatacagAAGCGTGATGATGCTCGACAGTTTATGAAGTTTCTTCATCCTGATCTTGGCGTTG
| ||| ||| || | || | | || | || || | | | ||||| || | | |||| ||| | | | | ||||| |||||||||||||| || || ||||||||||| |||||||||||||| ||||
tgtgtttttccctgaatttccttgacaccaattatggatctttggtat-gatttccagttaaaagtattgatagtagtctttctgaatctctcatt--tccagAAACGTGATGATGCTCGGCAATTCATGAAGTTTCTCCATCCTGATCTTGGTGTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccagctagtgaatgaaagtggactaacatgcattctcaattttttgtccatacagAAGCGTGATGATGCTCGACAGTTTATGAAGTTTCTTCATCCTGATCTTGGCGTTG
gactaac putative branch site (score: 1)
ttttttgtcc putative PPT
attctcaatttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taactttgccttctgttgcatggtcttagtcatttagctctgtttccagctagtgaatgaaagtggactaacatgcattctcaattttttgtccatacagAAGCGTGATGATGCTCGACAGTTTATGAAGTTTCTTCATCCTGATCTTGGCGTTG
- -ctttgcc
- - - - - ttctgtt
- - - - - - - - -gcatggt
- - - - - - - - - - - - - - - - - - - - tgtttcc
- - - - - - - - - - - - - - - - - - - - - - - - gctagtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acatgca