Sequence
atgc intronic sequence ATGC exonic sequence...aattgtaggttttgtctactcttccaacttctaaacaaattaaatattataatattttgatttcctattttcgtttcattttttttgggggtggggacagGCCATTCTTTCTGGGGAACCAAGTATTGTTGAGGCAGCTGCTGCATTGCTTAAGGCCATTGTTACCCGGAATCCCAAAGCTATGGTTCGTTTGTACAGCA
Basic information
species | Glycine max |
transcript | GLYMA05G08040.2 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G08040.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os10g42439.1 (Oryza sativa), 3'ss of exon 9
aattgtaggttttgtctactcttccaacttctaaacaaattaaatattataatattttgatttcc---tattttcgtttcattttttttgggggtggggacagGCCATTCTTTCTGGGGAACCAAGTATTGTTGAGGCAGCTGCTGCATTGCTTAAGGCCATTGTTACCCGGAATCCCAAAGCTATGGTTCGTTTGTACAGCA
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attctttcatattattt--ctttcttgcttttggatagttttatttttgtc-tacttctattatcgaacactgacaggaaatgataaatttgaaatggtatagGCTATGCTTACTGGGGAACCAAGCATTGTTGAAGCAGCTGCCTCATTACTTAAGGCTATTGTCACAAGAAACCCCAAAGCTATGATTCGACTATATAGTA
upper sequence: GLYMA05G08040.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G001895_T01 (Zea mays), 3'ss of exon 3
aattgtaggttttgtctactcttccaacttctaaacaaattaaatattataatattttgatttcctattttcgtttcat-tttttttgggggtgg----ggacagGCCATTCTTTCTGGGGAACCAAGTATTGTTGAGGCAGCTGCTGCATTGCTTAAGGCCATTGTTACCCGGAATCCCAAAGCTATGGTTCGTTTGTACAGCA
|||| | || | || | |||||| | | | || | | | |||||| | || || | | | | | |||| || ||| |||||||||| || || ||||| |||||||| ||||||||||||| |||||||| | ||||| ||||||||| |||| || || || |
--ttgt-gattcaatgatcttattcaacttttcat--atgtatttttctctttcttttgaacaatttcattgaccaaatgctgacaaaaaaattgcattgtatagGCTATGCTTACTGGGGAACCCAGCATCGTTGAAGCAGCTGCCTCATTGCTTAAGGCTATTGTTACAAGAAATCCTAAAGCTATGATTCGATTATATAGTA
upper sequence: GLYMA05G08040.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G049288_T01 (Zea mays), 3'ss of exon 9
--aattgtaggttttgtctactcttccaacttctaaacaaattaaatattataatattttgatttcctattttcgtttcattttttttgggggtggggacagGCCATTCTTTCTGGGGAACCAAGTATTGTTGAGGCAGCTGCTGCATTGCTTAAGGCCATTGTTACCCGGAATCCCAAAGCTATGGTTCGTTTGTACAGCA
| | | || | | || || | || | || || | ||| ||| | | | | | || | | | ||| || ||| ||||||||||||| |||||||| |||||||| ||||||||| ||| |||||||| | || || ||||||||| |||| || |||| |
tgattcaattatcttattcaacttttcagatg-tatgtttctctttcttttgaacaatttaattgaccaaatgc-tgacaaaaaacaaattgtattgtatagGTTATGCTTACTGGGGAACCAAGCATTGTTGAAGCAGCTGCCTCATTGCTTATGGCTATTGTTACAAGAAACCCTAAAGCTATGATTCGATTATACATTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attataatattttgatttcctattttcgtttcattttttttgggggtggggacagGCCATTCTTTCTGGGGAACCAAGTATTGTTGAGGCAGCTGCTGCATTGCTTAAGGCCATTGTTACCCGGAATCCCAAAGCTATGGTTCGTTTGTACAGCA
ttttgat putative branch site (score: 4)
aatattttgatttcct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aattgtaggttttgtctactcttccaacttctaaacaaattaaatattataatattttgatttcctattttcgtttcattttttttgggggtggggacagGCCATTCTTTCTGGGGAACCAAGTATTGTTGAGGCAGCTGCTGCATTGCTTAAGGCCATTGTTACCCGGAATCCCAAAGCTATGGTTCGTTTGTACAGCA
- - - -ggttttg
- - - - - - - - - ctcttcc
- - - - - - - - - - - - - - - - aaacaaa