Sequence
atgc intronic sequence ATGC exonic sequence...gtctattgtttgtttttaccttgaactcttgaaccaattgcttatctacattctgtattttcactttgctaatcggggttattatttttggatgaaatagGGAATCCTGAAGGCTTGGGCACTGAGCTGTTGGAAACCCTAGTAAAGATGGCTCCTACTAAAGAGGAAGAGATAAAACTCAAAAACTATGATGGTGATCT
Basic information
species | Glycine max |
transcript | GLYMA11G05220.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G05220.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g10680.1 (Oryza sativa), 3'ss of exon 2
gtctattgtttgtttttaccttgaactcttgaaccaattgcttatctacattctgtattttcactttgctaatcggggttattatttttggatgaaatagGGAATCCTGAAGGCTTGGGCACTGAGCTGTTGGAAACCCTAGTAAAGATGGCTCCTACTAAAGAGGAAGAGATAAAACTCAAAAACTATGATGGTGATCT
| | | || ||| | || | | | | |||| | | || | || | || |||| || | | ||| ||| ||||| || |||| | ||| || |||||||| |||| |||||||||||||||||||||||||| | ||||| | |||| |||||| |
ttttttcattgcggcatactgtaaatctgtaatttagtatgccatctctacatgagggtgtccagtgaatatgtgtaatttctattgttcttttgagcagGCAATGCTGAATGCCTGGGGAGTGAACTTTTGGAAACATTAGTCAAGATGGCTCCTACTAAAGAGGAAGAACTGAAACTACGAGACTACAGTGGTGACTT
upper sequence: GLYMA11G05220.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os10g20710.1 (Oryza sativa), 3'ss of exon 2
-----gtctat-tgtttgtttttaccttgaactcttgaaccaattgcttatctacattctgtattttcactttgctaatcggggttattatttttggatgaaatagGGAATCCTGAAGGCTTGGGCACTGAGCTGTTGGAAACCCTAGTAAAGATGGCTCCTACTAAAGAGGAAGAGATAAAACTCAAAAACTATGATGGTGATCT
| || | | | || | ||| | || ||| ||| | || || | | | ||| | | || || | || ||||||| ||| ||||| | ||||| |||| || ||||| ||| |||||||||||||||| || ||||||||||| | ||||| | | | ||| || |
aatacagcaatacacacctctcagcgatgcagaattggataaa--aactataaacactttgcatcta-attccagtaaccata--tgttgttcatctat-aaatagGTAATGCTGAATGTTTGGGAGCTGAACTTTTGGAGACCTTAGTAAAGATGGCTCCAACCAAAGAGGAAGAACTGAAACTGCGAGATTTCACTGGGGACTT
upper sequence: GLYMA11G05220.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G090693_T01 (Zea mays), 3'ss of exon 2
gtctattgttt--gtttttaccttgaactcttgaaccaattgcttatctacattctgtattt--tcactttgctaatcggggttattatttttggatgaaatagGGAATCCTGAAGGCTTGGGCACTGAGCTGTTGGAAACCCTAGTAAAGATGGCTCCTACTAAAGAGGAAGAGATAAAACTCAAAAACTATGATGGTGATCT
|| || | | | | | | | || || | || | ||| ||| | | |||| || | || | | | ||| || ||| ||| ||| ||||| || |||| | || ||||||||||| | ||||||||||||||||| ||||||||||| | || || ||||| | || ||
acatactgctccaggatgtgcagtcagctacatgacagcattctaaactattgtctagttctactcacaatgtttattgctgctgacattcttt----aaacagGCAATGCTGAATGCCTGGGTGCGGATTTGTTGGAAACCTTGGTAAAGATGGCTCCTACGAAAGAGGAAGAACTGAAGCTTCGAAACTTTACCGGGGACTC
upper sequence: GLYMA11G05220.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G429928_T01 (Zea mays), 3'ss of exon 1
gtctattgtttgtttttaccttgaactcttgaaccaattgcttatctacattctgtattttcactttgctaatcggggttattatttttggat------gaaatagGGAATCCTGAAGGCTTGGGCACTGAGCTGTTGGAAACCCTAGTAAAGATGGCTCCTACTAAAGAGGAAGAGATAAAACTCAAAAACTATGATGGTGATCT
| | | | | || | | | || | | | | |||||||| | | | || | | |||| | ||| ||| ||| || ||||| || |||| | || |||||||||||| | | ||||||||||||||| |||||||||||| | |||||| |||| ||| ||| |
--caaatacatactgtt--cacagaatgttcagtgacctac--atctacatgacagcatccaaagctactcacaacgtctattgctactggcactgttaaaaacagGCAACGCTGAATGCCTGGGGGCGGATCTGTTGGAAACCTTGGCAAAGATGGCTCCTACAAAAGAGGAAGAGCTCAAACTCCGCAACTTCACTGGGGATAT
upper sequence: GLYMA11G05220.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM5G872264_T01 (Zea mays), 3'ss of exon 3
gtctattgtttgtttttacc--ttgaactcttgaaccaattgcttatctacattctgtattttcactttgctaatcggggttattatttttggatgaaatagGGAATCCTGAAGGCTTGGGCACTGAGCTGTTGGAAACCCTAGTAAAGATGGCTCCTACTAAAGAGGAAGAGATAAAACTCAAAAACTATGATGGTGATCT
||| ||| | ||||| | || || || || | | | || | | | | | | | | | || || | | || ||| ||| || ||||| ||||| ||||| || ||||| || |||| |||||||||||||||||||||||||| | ||||| || | ||| ||| |||
-tctgttgct-gttttagctgttttgacgtttaaaatataaatctctataaaatatagctcataaaccattaatttgtcatttctactgtattattaaacagGCAACACTGAATATTTGGGGACTGAACTTTTGGAGACTTTAGTCAAGATGGCTCCTACTAAAGAGGAAGAACTCAAACTACAAGATTATAATGATGACAC
upper sequence: GLYMA11G05220.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G075921_T01 (Zea mays), 3'ss of exon 2
gtctattgt-ttgtttttacc-ttgaactcttgaaccaattgcttatctacattctgtattttcactttgctaatcggggttattatttttggatgaaatagGGAATCCTGAAGGCTTGGGCACTGAGCTGTTGGAAACCCTAGTAAAGATGGCTCCTACTAAAGAGGAAGAGATAAAACTCAAAAACTATGATGGTGATCT
| |||| || ||| || | || || | | | || | | | | | | | || || | | || ||| ||| || ||||| | ||||| || || || ||||| || |||| |||||||||||||||||||||||||| | | ||| | | ||| |||||||
--ccattgcattaggcctactatttgatgtttaaaatataaatctttataaaatagagctcatggggcattaatttgtcatttctactgtattatcaaacagGCAACGCTGAATGTTTGGGGACAGAACTTTTGGAGACTTTAGTCAAGATGGCTCCTACTAAAGAGGAAGAACTCAGACTACGAGATTATAATGGTGACGC
upper sequence: GLYMA11G05220.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv07s0129g00220.t01 (Vitis vinifera), 3'ss of exon 2
----gtctattgtttgtttttaccttga-actcttgaaccaattgcttatctacattctgtattttcactttgctaatcggggttattatttttggatgaaatagGGAATCCTGAAGGCTTGGGCACTGAGCTGTTGGAAACCCTAGTAAAGATGGCTCCTACTAAAGAGGAAGAGATAAAACTCAAAAACTATGATGGTGATCT
| | || | | | | || | || | | |||||| | | || | || | | |||| | | |||||||| || ||| || || ||| ||||||| ||||||| |||||||| |||||||||||||||| || || |||||||| |||||||| | | || |||||| |
gaattaaaacagattatatgtccattaatgttcatttaatgcttgctt-tgcaaataattgtttgtggggatcctaagtga----aatatttttgtctgtggcagGTAACCCAGAAAGCTTGGGTGCTGAGCTTTTGGAAACTTTAGTAAAGATGGCTCCCACCAAGGAGGAAGAAATAAAACTTCGAGATTACAGTGGTGACAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctacattctgtattttcactttgctaatcggggttattatttttggatgaaatagGGAATCCTGAAGGCTTGGGCACTGAGCTGTTGGAAACCCTAGTAAAGATGGCTCCTACTAAAGAGGAAGAGATAAAACTCAAAAACTATGATGGTGATCT
tgctaat putative branch site (score: 2)
ttattatttttggatg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctattgtttgtttttaccttgaactcttgaaccaattgcttatctacattctgtattttcactttgctaatcggggttattatttttggatgaaatagGGAATCCTGAAGGCTTGGGCACTGAGCTGTTGGAAACCCTAGTAAAGATGGCTCCTACTAAAGAGGAAGAGATAAAACTCAAAAACTATGATGGTGATCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - tgtttgt
- - - - - - - - - ccttgaa
- - - - - - - - - -cttgaac
- - - - - - - - - - - - - - - - - caattgc
- - - - - - - - - - - - - - - - - - - - - - - - cattctg