Sequence
atgc intronic sequence ATGC exonic sequence...tttgcattttgcttagtcaaatttaaattttcttggcgtggtatctgttgtatgattgaaagttactgagctaaatgtaatgtgtcttttctttgagcagGTCAAAATTTGGTGCACTAATCAGGAAGCTAGTGTTCTAAATATAGACATGAAAGCAAACATATGTTGTGTCAAATATAATCCTGGATCTGGCAATTATA
Basic information
species | Glycine max |
transcript | GLYMA02G43540.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G43540.2 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G104920_T02 (Zea mays), 3'ss of exon 8
-tttgcattttgctta--gtcaaatttaaattttcttggcgtggtatctgttgtatgattgaaagttactgagctaaatgtaatgtgtcttttctttg-agcagGTCAAAATTTGGTGCACTAATCAGGAAGCTAGTGTTCTAAATATAGACATGAAAGCAAACATATGTTGTGTCAAATATAATCCTGGATCTGGCAATTATA
| ||| | | | || | | | || |||| || || || | | | | | || || | | | || || ||| |||||| ||| | |||||||| ||||| ||||| ||||| | ||||| || ||||||||||| || || | || ||||||||||||||||| || ||
atgaatattaagttcatgaacacaacaacagatttttggtgt---atgcatttt-caagtaaggacaaaaaagaagaaataattacggctgttgtttatggcagGTGAAAGTGTGGTGCACAAATCAAGAAGCAAGTGTGATCAATATTGATATGAAAGCAAATATTTGCTCGGTTAAATATAATCCTGGATCAAGCTTCTACG
upper sequence: GLYMA02G43540.2 (Glycine max), 3'ss of exon 9
lower sequence: AT2G32950.1 (Arabidopsis thaliana), 3'ss of exon 9
tttg---cattttgct--tagtcaaatttaaattttcttggcgtggtatctgttgtatgattgaaagttactgagctaaatgtaatgtgtcttttctttgagcagGTCAAAATTTGGTGCACTAATCAGGAAGCTAGTGTTCTAAATATAGACATGAAAGCAAACATATGTTGTGTCAAATATAATCCTGGATCTGGCAATTATA
||| || || || |||| || | || | | | ||||||| || || | | | | || ||| ||||| ||| | ||||| ||| |||||||||| | |||||||| ||||| | ||||| || |||||||||||||||||||||||||| || |||||||| || |||| || |
tttaagtcaattcactactagttaatcctcaaccatgc-attattgcatctgttaaatcatgtctcatagattaaccaattgtgctgtgtgtttgatc----cagGTTAAAGTTTGGTGCACGAGGCAGGAAGCAAGTGTGATTAATATTGATATGAAAGCAAACATATGTTGTGTCAAGTACAATCCTGGCTCAAGCAACTACA
upper sequence: GLYMA02G43540.2 (Glycine max), 3'ss of exon 9
lower sequence: Vv12s0059g01420.t01 (Vitis vinifera), 3'ss of exon 9
tttgcattttgcttagtcaaatttaaattttcttggcgtggtatctgttgtatgattgaaagttactgagctaaatgtaatgtgtcttttctttgagcagGTCAAAATTTGGTGCACTAATCAGGAAGCTAGTGTTCTAAATATAGACATGAAAGCAAACATATGTTGTGTCAAATATAATCCTGGATCTGGCAATTATA
| |||| | | || | | | | | || | || | | | | |||| | ||| | | | | | | | ||||||||| |||||||||| || ||||| ||||| ||||| || || |||||||||||||| |||||||||||||| ||||||||||||||| ||| |||||
agttcattataatcagggtactggggactccatattggtttgacatgctaaactaaccatagtttgtatctgttatgaacttaatgtatgtaataaacagGTCAAAGTTTGGTGCACAAACCAGGAGGCTAGCGTTCTTAACATTGACATGAAAGCAAATATATGTTGTGTCAAGTATAATCCTGGATCTAGCATTTATA
upper sequence: GLYMA02G43540.2 (Glycine max), 3'ss of exon 9
lower sequence: PP1S25_325V6.1 (Physcomitrella patens), 3'ss of exon 9
tttgcattttgcttagtcaaatttaaattttcttggcgtggtatctgttgtatgattgaaagttac-tgagctaaatgtaatgtgtcttttctttgagcagGTCAAAATTTGGTGCACTAATCAGGAAGCTAGTGTTCTAAATATAGACATGAAAGCAAACATATGTTGTGTCAAATATAATCCTGGATCTGGCAATTATA
||||| || | | | | | | | | | || ||||| | | | | ||| | | || |||||| || ||||||||||||||||||| ||||||||| | | |||||||||||| || ||||| || || || || || |||||||| || |||| |||
cccatgttttggttgcacgattacgggggaatataacagagactgtctcgt-tgattcttactcaagtcagccgttaaaagcagatggggggattttgcagGTTAAGCTTTGGTGCACTAATCAGGAGGCTAGTGTTTTTAGTATAGACATGAAGGCCAACATCTGCTGCGTTAAGTACAATCCTGGTTCAAGCAACCATA
upper sequence: GLYMA02G43540.2 (Glycine max), 3'ss of exon 9
lower sequence: PP1S135_17V6.1 (Physcomitrella patens), 3'ss of exon 9
--------------------------------------------------tttgcatttt--gcttagtcaaatttaaattttcttggcgtggtatctgttgtatgattgaaa-gttactgagctaaatgtaatgtgtcttttctttgagcagGTCAAAATTTGGTGCACTAATCAGGAAGCTAGTGTTCTAAATATAGACATGAAAGCAAACATATGTTGTGTCAAATATAATCCTGGATCTGGCAATTATA
| || ||| |||| ||||| | | || | |||| || | || | ||| || | | | ||| | || | | | || || | |||||| || || |||||||| | || || | || || |||||||||||||||| ||||| || || ||||| || |||||||||||||| ||| |||
gtaacctgttgaaatctggtgaacttaatcactcttgtacttgatgcggttctgtttttcaagctttttcaaactcaggttat-ttggagt--tttccgcatcatgtttaatatgcggttgatccgaa-atgtttttatgttactgtttgcagGTGAAGATATGGTGCACGAGGCAAGAGTCAAGCGTGATAAATATAGACATGAAGGCAAATATTTGCTGTGTGAAGTATAATCCTGGATCAAGCAGCTATG
upper sequence: GLYMA02G43540.2 (Glycine max), 3'ss of exon 9
lower sequence: EFJ20512 (Selaginella moellendorffii), 3'ss of exon 9
tttgcattttgcttagtcaaatttaaattttcttggcgtggtatctgttgtatgattgaaagttactgagctaaatgtaatgtgtcttttctt--tgagcagGTCAAAATTTGGTGCACTAATCAGGAAGCTAGTGTTCTAAATATAGACATGAAAGCAAACATATGTTGTGTCAAATATAATCCTGGATCTGGCAATTATA
||| | ||| | |||| | | ||| ||| | | || || | |||||||| | |||||||| | ||||| | ||||| || || || |||||||| |||||||| || ||||||||||| ||||| |||||| |||||| |
-----------------------------------------------gtgttttattattacttacacacccgaattccctgtttgtgtttttgacgcacagGTCAAGCTGTGGTGCACCAGGCAGGAGACAAGTGTCCTGAACATTGACATGAAGGCAAACATTTGCTGTGTCAAATACAATCCCGGATCTAGCAATTTTG
upper sequence: GLYMA02G43540.2 (Glycine max), 3'ss of exon 9
lower sequence: EFJ28584 (Selaginella moellendorffii), 3'ss of exon 9
tttgcattttgcttagtcaaatttaaattttcttggcgtggtatctgttgtatgattgaaagttactgagctaaatgtaatgtgtcttttctt--tgagcagGTCAAAATTTGGTGCACTAATCAGGAAGCTAGTGTTCTAAATATAGACATGAAAGCAAACATATGTTGTGTCAAATATAATCCTGGATCTGGCAATTATA
| ||| | ||| | |||| | | ||| | ||| | | || || | |||||||| | |||||||| | ||||| | ||||| || || || |||||||| |||||||| || ||||||||||| ||||| |||||| |||||| |
--------------------------------------------gtagtgttttattattacttacacacccgaattcactgtttgtgtttttgacgcacagGTCAAGCTGTGGTGCACCAGGCAGGAGACAAGTGTCCTGAACATTGACATGAAGGCAAACATTTGCTGTGTCAAATACAATCCCGGATCTAGCAATTTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttgtatgattgaaagttactgagctaaatgtaatgtgtcttttctttgagcagGTCAAAATTTGGTGCACTAATCAGGAAGCTAGTGTTCTAAATATAGACATGAAAGCAAACATATGTTGTGTCAAATATAATCCTGGATCTGGCAATTATA
agctaaa putative branch site (score: 3)
tgtgtcttttcttt putative PPT
taaatgtaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttgcattttgcttagtcaaatttaaattttcttggcgtggtatctgttgtatgattgaaagttactgagctaaatgtaatgtgtcttttctttgagcagGTCAAAATTTGGTGCACTAATCAGGAAGCTAGTGTTCTAAATATAGACATGAAAGCAAACATATGTTGTGTCAAATATAATCCTGGATCTGGCAATTATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- tgcattt
- - - - -tgcttag
- - - - - - - - - - - - - - - - - ggcgtgg
- - - - - - - - - - - - - - - - - - - - - - - - tgtatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttactg