Sequence
atgc intronic sequence ATGC exonic sequence...cttttaggatccaattcgtttttgataacctcattttgcatccttgatggcatggcaattcaagaatcctagatcctaacgtctgtcattgcctctgcagGTTCTGTGTTCTTAGGGCCTTGGACTCCTGAGAGTGTTGGTGATTATGCAAGTGGGACAAACCATGTCCTTCCTACTTACGGTTATGCAAGAATGTATGG
Basic information
species | Glycine max |
transcript | GLYMA09G02960.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G02960.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os01g13190.1 (Oryza sativa), 3'ss of exon 12
cttttaggatccaattcgtttttgataacctcattttgcatccttgatggcatggcaattcaagaatcctagatcctaacgtctgtcattgcctctgcagGTTCTGTGTTCTTAGGGCCTTGGACTCCTGAGAGTGTTGGTGATTATGCAAGTGGGACAAACCATGTCCTTCCTACTTACGGTTATGCAAGAATGTATGG
| || | | | | | || ||| ||| | | | ||||| | | | || || || | || |||| || || ||||| || | ||||| || ||||| || || || |||||||| || ||||||||||||||||| || || ||||| ||||| |||||| |
------gtataggcatacctgtcagcgtcttaatcttga--cctgaacattttcatacttcaatggt---aatctcaggcgatcgttttttcatc-acagGGTCGGTCTTCTTGGGACAATGGACCCCGGAGAGCGTGGGCGACTATGCAAGCGGCACAAACCATGTCCTTCCAACCTATGGTTACGCAAGGATGTATAG
upper sequence: GLYMA09G02960.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G058584_T01 (Zea mays), 3'ss of exon 14
-----------cttttaggatccaattcgtttttgataacctcattttgca---------tccttgatggcatggcaattcaagaatcctagatcctaacgtctgtcattgcctctgcagGTTCTGTGTTCTTAGGGCCTTGGACTCCTGAGAGTGTTGGTGATTATGCAAGTGGGACAAACCATGTCCTTCCTACTTACGGTTATGCAAGAATGTATGG
|||| | | | | || | || | || | || | | ||| |||| |||| || |||| || | || | | |||| || || ||||| || | ||||| || ||||| || || |||||||| || ||||| |||||||||||||| || || ||||| ||||| ||||| |
gtaggcatattttttttgtcattagctttggtgtggtcacattgttcttcaagcagatggttccccttggggcatcaatctt-gaattcttgatcgaaatatttggtttctttacctcagGGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGAGCGGGACGAACCATGTCCTTCCGACCTATGGTTACGCAAGGATGTACAG
upper sequence: GLYMA09G02960.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv18s0166g00300.t01 (Vitis vinifera), 3'ss of exon 14
cttttaggatccaattcgtttttgataacctcattttgcatccttgatggca--tggcaattcaagaatcctagatcctaacgtctgtcattgcctctgcagGTTCTGTGTTCTTAGGGCCTTGGACTCCTGAGAGTGTTGGTGATTATGCAAGTGGGACAAACCATGTCCTTCCTACTTACGGTTATGCAAGAATGTATGG
||| || || | | | || | | | || | ||| || | ||||| || || | | | | ||||||||||||||||||| ||||||| ||||| || || ||||| || |||||||||||||| ||||||||||||||||| || || || |||||| | ||||||||
tgattaagaaa-aacaagagaccatgcagcccagtcaataactatgtttatcactggtgtttttataatccagcctcatatcatttacttct-cctctgcagGTTCTGTGTTTTTAGGGCAGTGGACACCGGAAAGTGTGGGGGATTATGCAAGTGGAACAAACCATGTCCTTCCAACATATGGCTATGCACGGATGTATGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatggcatggcaattcaagaatcctagatcctaacgtctgtcattgcctctgcagGTTCTGTGTTCTTAGGGCCTTGGACTCCTGAGAGTGTTGGTGATTATGCAAGTGGGACAAACCATGTCCTTCCTACTTACGGTTATGCAAGAATGTATGG
tcctaac putative branch site (score: 1)
ttgcctct putative PPT
aattcaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttttaggatccaattcgtttttgataacctcattttgcatccttgatggcatggcaattcaagaatcctagatcctaacgtctgtcattgcctctgcagGTTCTGTGTTCTTAGGGCCTTGGACTCCTGAGAGTGTTGGTGATTATGCAAGTGGGACAAACCATGTCCTTCCTACTTACGGTTATGCAAGAATGTATGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - -ttttgca
- - - - - - - - - - - - - - - - - - - - - - - - -gcatggc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctgtca