Sequence
atgc intronic sequence ATGC exonic sequence...aaacatcactattgtttccttactttactgctttcaatatttatctgttaggttcccttatgtttgataatttcttataaaattctggatctttctccagCTTGGTGAAACCATTTGCCCGATGAAGGAAGATTTTATTATGGTTCATTTGCAGCATGCATGTACTAGCTGTTGTATTTTAATGGTGTCTGGCAACCGTT
Basic information
species | Glycine max |
transcript | GLYMA07G00230.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G00230.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os02g04490.1 (Oryza sativa), 3'ss of exon 12
--------------------------------------------------------aaacatcactattgtttccttactttactgctttcaatatttatctgttaggttcccttatgtttgataatttctt-ataaaattctggatctttc---tccagCTTGGTGAAACCATTTGCCCGATGAAGGAAGATTTTATTATGGTTCATTTGCAGCATGCATGTACTAGCTGTTGTATTTTAATGGTGTCTGGCAACCGTT
|| || | ||||| | | || | | ||| |||| ||| ||| | | ||| |||| | | || ||| | | | |||||||| |||||||||| || |||||||||||||| |||||||||||||||||| || | |||| | |||||||| | ||||||||||| || ||||
gtaggattgtacagtggtttgcgtgctccttattttgatagatcacatggctgctagcactctacccctctttccct-ttctatcatccttgctcagtatttgtttttttcactt-tactggatggcatctttaccatgaacttgatttgttatgtgcagCTTGGGGAAACCATTTATCCAATGAAGGAAGATTTCATTATGGTTCATTTGCAGTATTCGTGTAGTCACTGTTGTACCCTTATGGTGTCTGGAAAACGTT
upper sequence: GLYMA07G00230.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G470556_T01 (Zea mays), 3'ss of exon 11
--------------------------------------aaacatc----actattgtttccttactttactgctttcaatatttatctgttaggttcccttatgtt-tgataatttcttataaaattctggatctttc--tccagCTTGGTGAAACCATTTGCCCGATGAAGGAAGATTTTATTATGGTTCATTTGCAGCATGCATGTACTAGCTGTTGTATTTTAATGGTGTCTGGCAACCGTT
||| | | ||| | || | | | | | | | | | ||| | | || || | ||||| || | ||| | | | | | ||||||||||||||||| | || |||||||||||||| |||||||| ||||||||| || |||||| | ||| |||| | ||||||||||| | ||||
gtaagcttctttgatttctgtgtacttcctgctctcataaatactctaaagtatactcctgttcttctctcccaccctaagtctcttttttacatacttgaattttatattaattgggtaacacattttaattttgtgcatgcagCTTGGTGAAACCATATATCCTATGAAGGAAGATTTCATTATGGTCCATTTGCAGTATTCATGTAGTCACTGCTGTACCCTTATGGTGTCTGGAAGACGTT
upper sequence: GLYMA07G00230.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G139977_T01 (Zea mays), 3'ss of exon 11
---------------------------------------------------aaacatcactattgtttccttactttactgctttcaatatttatctgttaggttcccttatgtttgataat-ttcttataaaattctggatc-tttctccagCTTGGTGAAACCATTTGCCCGATGAAGGAAGATTTTATTATGGTTCATTTGCAGCATGCATGTACTAGCTGTTGTATTTTAATGGTGTCTGGCAACCGTT
||| | || | | | | || | | | | | ||| | | | | | ||| || | | ||| ||| | | | | ||||||||||||||||| | || |||||||||||||| |||||||| ||||| ||| || | |||| | |||||||| | ||||||||||| | ||||
gtaagcttctttgatttctgtgtacttcctgctctcataaataaatactcaaaaaaagtatactcctgcttctctctcccaccctgtctcttt-tttacttgaattttgtatattgggcgacacatttaccgtgctctattttgtgtatgcagCTTGGTGAAACCATATATCCTATGAAGGAAGATTTCATTATGGTCCATTTACAGTATTCGTGTAGTCACTGTTGTACCCTTATGGTGTCTGGAAGACGTT
upper sequence: GLYMA07G00230.1 (Glycine max), 3'ss of exon 12
lower sequence: AT1G55970.1 (Arabidopsis thaliana), 3'ss of exon 11
aaacatcactattgtttccttactttactgctttcaatatttatctgttaggttcccttatgtttgataatttcttataaaattctggatctttctccagCTTGGTGAAACCATTTGCCCGATGAAGGAAGATTTTATTATGGTTCATTTGCAGCATGCATGTACTAGCTGTTGTATTTTAATGGTGTCTGGCAACCGTT
| |||| || |||| ||| || ||| | | ||| | | || | | | | | | ||||| |||| ||||| |||||||| |||||||||||||||||||| |||||||||||||| ||| || | ||| | | | ||||| ||||| ||||| |
------------------gtaactt--cttatttctccattccactattatgat--cttgcttccaccagcttttatttatttgttctgtttttctgtagCTCGGTGAGACCATTTGTCCGATGAAGGAAGATTTTATAATGGTTCATTTGCAACATTGCTGCAAGCATTGTACCACTCTCATGGTATCTGGAAACCGGT
upper sequence: GLYMA07G00230.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv09s0054g01780.t01 (Vitis vinifera), 3'ss of exon 11
----aaacatcactattgtttccttactttactgctttcaatatttatctgtt--aggttcccttatgtttgataatttcttataaaattctggatctttctccagCTTGGTGAAACCATTTGCCCGATGAAGGAAGATTTTATTATGGTTCATTTGCAGCATGCATGTACTAGCTGTTGTATTTTAATGGTGTCTGGCAACCGTT
|||| || | || | || ||| || || || | || | | | | || || |||||| ||||||| || | | || |||||||||||||||||||||| |||| ||||||||||||||||| |||||||| ||||| |||||||||||| |||||| | | ||||| ||||| |||||||
tttcaaacgtcttcactgatattatatttt-ctcctgacacttttgaacaaatgaaagtcaatttctgtttg-----ttcttatgaagctatctattcttctccagCTTGGTGAAACCATAAGCCCAATGAAGGAAGATTTTATAATGGTTCACTTGCAACATGCATGTACTCATTGTTGTCATCTGATGGTATCTGGAAACCGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttaggttcccttatgtttgataatttcttataaaattctggatctttctccagCTTGGTGAAACCATTTGCCCGATGAAGGAAGATTTTATTATGGTTCATTTGCAGCATGCATGTACTAGCTGTTGTATTTTAATGGTGTCTGGCAACCGTT
gtttgat putative branch site (score: 5)
tctttctcc putative PPT
ttatgtttgataattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaacatcactattgtttccttactttactgctttcaatatttatctgttaggttcccttatgtttgataatttcttataaaattctggatctttctccagCTTGGTGAAACCATTTGCCCGATGAAGGAAGATTTTATTATGGTTCATTTGCAGCATGCATGTACTAGCTGTTGTATTTTAATGGTGTCTGGCAACCGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- acatcac
- - - - - - tgtttcc
- - - - - - - - - - - - - - tgctttc
- - - - - - - - - - - - - - - - - - - - - - ctgttag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -attctgg