Sequence
atgc intronic sequence ATGC exonic sequence...ttaaatagaattcattctctcacaacttagactatgaataactcatgttgcttcatgtcattgacttgaatatatgcgacttttccttgtgtacaaacagTGCTGCTGTATTCCACAATGCAAGTACGCGGTTTTGTGATGGAGCACGCTTTGGGCTTGGTGCAGAG
Basic information
species | Glycine max |
transcript | GLYMA03G12240.1 |
intron # | 17 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G12240.1 (Glycine max), 3'ss of exon 17
lower sequence: LOC_Os01g62900.1 (Oryza sativa), 3'ss of exon 17
ttaaatagaattcattctctcacaacttagactatgaataactcatgttgcttcatgtcattgacttgaatatatgcgacttttccttgtgtacaaacagTGCTGCTGTATTCCACAATGCAAGTACGCGGTTTTGTGATGGAGCACGCTTTGGGCTTGGTGCAGAG
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--gtgtttaactaatttcctttgcacaactattatgtttgccgctt-ttagtacatacc-ttaatt--aatgga-gttattcttctataaattgcaacagTGCTGCGGTATTCCATAATGCAAGCACACGGTTCTGTGATGGGGCTCGCTTTGGTCTAGGTGCTGAG
upper sequence: GLYMA03G12240.1 (Glycine max), 3'ss of exon 17
lower sequence: LOC_Os05g38150.1 (Oryza sativa), 3'ss of exon 16
----------------------------ttaaatag--aattcattctctcacaacttagactatgaataact-catgttgcttcatg-tcattg---acttgaata-tatgcgacttttccttgtg-tacaaacagTGCTGCTGTATTCCACAATGCAAGTACGCGGTTTTGTGATGGAGCACGCTTTGGGCTTGGTGCAGAG
| ||| | | | ||| || | | | | | | | || | | ||| | ||| | | | || | || | | | | | | | | ||||||||||||||||| || |||||||||||| | || | |||||| || || ||||| | ||||| |||
gtatgtttaaacattaattcccttattacttaatggttacattatttgttccctattgatgc-acaattattttcctgtcaacttatgatgaacggatgtttaactaatgttctgttctacttctcaatttgaacagTGCTGCTGTATTTCATAATGCAAGTACGAGATTCTCTGATGGGGCTCGTTTTGGATTGGGTGCTGAG
upper sequence: GLYMA03G12240.1 (Glycine max), 3'ss of exon 17
lower sequence: Vv08s0007g01060.t01 (Vitis vinifera), 3'ss of exon 17
-ttaaatagaattcattctctcacaacttagactatgaataactcatgttgcttcatgtcattgacttgaatat---atgcgacttttccttgtgtacaaacagTGCTGCTGTATTCCACAATGCAAGTACGCGGTTTTGTGATGGAGCACGCTTTGGGCTTGGTGCAGAG
|||| ||| ||| | | || || || || | ||| | || | ||| || | | ||| | || | | | | ||||||||||| || ||||| ||||||||||| || ||||||||||||||||| ||||| ||||||||||||
tacaaatgcaat--ggtctgtaaattgtttgagta-atttatgctaaattgttgcacatatttgtgttaaccttgaaatgtggctcattatc-tatctcaacagTGCTGCAGTTTTCCATAATGCAAGTACCCGATTTTGTGATGGAGCACGTTTTGGACTTGGTGCAGAG
upper sequence: GLYMA03G12240.1 (Glycine max), 3'ss of exon 17
lower sequence: PP1S22_40V6.2 (Physcomitrella patens), 3'ss of exon 17
---ttaaatagaattcattctctcacaacttagactatgaataactcatgttgcttcatgtcattgacttgaatatatgcgacttttccttgtgtacaaacagTGCTGCTGTATTCCACAATGCAAGTACGCGGTTTTGTGATGGAGCACGCTTTGGGCTTGGTGCAGAG
| || | || ||| | | | | ||| | || || | | ||||||| | | || | | | | | | |||||| |||||||| || ||||| ||||| || |||| |||||| || || |||||||||||||| |||
taccttcattgcgctctctcttttgcttgtaatactgttcgtattgtattcaggct---gtcattgttgtaacattaaataatactgcttgcttcatttgcagTGCCGCTGTATTTCATAATGCCAGTACCCGCTTTTCTGATGGTGCTCGTTTTGGGCTTGGTGCTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttgcttcatgtcattgacttgaatatatgcgacttttccttgtgtacaaacagTGCTGCTGTATTCCACAATGCAAGTACGCGGTTTTGTGATGGAGCACGCTTTGGGCTTGGTGCAGAG
cattgac putative branch site (score: 3)
ttgaatatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttaaatagaattcattctctcacaacttagactatgaataactcatgttgcttcatgtcattgacttgaatatatgcgacttttccttgtgtacaaacagTGCTGCTGTATTCCACAATGCAAGTACGCGGTTTTGTGATGGAGCACGCTTTGGGCTTGGTGCAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- aaatagaa
- - - - - - - - ctctcac
- - - - - - - - - - - - - - - -ctatgaa
- - - - - - - - - - - - - - - - - - - - - - -tgttgct
- - - - - - - - - - - - - - - - - - - - - - - - - - tcatgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgacttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatatgc