Sequence
atgc intronic sequence ATGC exonic sequencegtgagtgcttcatctcacttgtggggaaaaaaacaattaaaatcaaatttatggactaaaatggtggtagaaatgttgtgatccacatgattgcttatttgtgtatttctttgtctcagGCACGTTCTCCACAAGTATGCCAATGAGGATGTCTCACTAGGTTCTTGGTTTATTGGACTTGATGTGAATCACATAGATGATCGAAGACTCTGCTGTGGT
Basic information
species | Glycine max |
transcript | GLYMA13G38500.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G38500.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os03g38050.1 (Oryza sativa), 3'ss of exon 9
gtgagtgcttcatctcacttgtggggaaaaaaac--aattaaaatcaaatttatggactaaaatggtggtagaaatgttgtgatc----cacatgattgcttatttgtgtatttctttgtctcagGCACGTTCTCCACAAGTATGCCAATGAGGATGTCTCACTAGGTTCTTGGTTTATTGGACTTGATGTGAATCACATAGATGATCGAAGACTCTGCTGTGGT
|| | || ||| | ||| | || || | | || | | | | | | ||| |||| || || || ||| ||||||| ||||||||||| ||||| ||||||||||| ||| |||| | ||||| || || || || || | ||| | |||||||| || || ||||| |||
--------------------gtaagaaatttcttcagatttggtttttctttgttgattacacca-taatatgttttatctaacctctacccatcattgaccatggatg-atggtgatgtttcagGCATGTTCTCCACAAATATGCTAATGAGGATGTATCATTAGGAGCATGGTTCATAGGTCTAGACGTCGAACACGTCGATGATCGCAGGCTTTGCTGCGGT
upper sequence: GLYMA13G38500.1 (Glycine max), 3'ss of exon 9
lower sequence: AT2G32430.1 (Arabidopsis thaliana), 3'ss of exon 9
gtgagtgcttcatctcacttgtggggaaaaaaacaattaaaatcaaatttatggactaaaatggtggtagaaatgttgtgatccacatgattgcttatttgtgtatttctttgtctcagGCACGTTCTCCACAAGTATGCCAATGAGGATGTCTCACTAGGTTCTTGGTTTATTGGACTTGATGTGAATCACATAGATGATCGAAGACTCTGCTGTGGT
| | |||| | ||| || | | || || || || | || | | ||| |||||| ||||| ||||| ||||| ||||||||||| || ||||| |||||||||| || |||||||||| || || |||||| ||||||| || |||||
-----------------------------------------gtaagattt--gaactcctttg-taccgcatcatttatgcctcattctccatctaacttctcttacaaaatgttccagGCATGTTCTGCACAAATATGCAAATGAGGATGTTACATTAGGTGCTTGGTTTATCGGGCTTGATGTGACACATATCGATGATAGAAGACTATGTTGTGGC
upper sequence: GLYMA13G38500.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G05170.2 (Arabidopsis thaliana), 3'ss of exon 9
gtgagtgcttcatctcacttgtggggaaaaaaacaattaaaatcaaatttatggactaaaatg-gtggtagaaatgttgt-gatccacatgattgcttatttgtgtatttctt---tgtctcagGCACGTTCTCCACAAGTATGCCAATGAGGATGTCTCACTAGGTTCTTGGTTTATTGGACTTGATGTGAATCACATAGATGATCGAAGACTCTGCTGTGGT
||| || || | | || || | || | ||| |||| | || | | | | || | || | || ||| ||||||| ||||| ||||||||||| || || ||||| || ||||| |||||||||| || ||||||| || ||||| |||||| ||||| | ||||| ||
------------------------------------gtaagatgaagatga--gattacattgtatcatagctcatttgttaactcatgtaactcttcgttcttatacatgttaaatgtttcagGCATGTTCTTCACAAGTATGCGAACGAAGATGTTTCGCTAGGAGCTTGGTTTATCGGGATTGATGTTAAACACATTGATGATAGAAGATTATGCTGCGGA
upper sequence: GLYMA13G38500.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv12s0059g00640.t01 (Vitis vinifera), 3'ss of exon 9
gtgagtgctt-catctcacttgtggggaaaaaaacaattaaaatcaaatttatggactaaaatggtggtagaaatgttgtgatccacatgat-tgcttatttgtgtatttctttgtctcagGCACGTTCTCCACAAGTATGCCAATGAGGATGTCTCACTAGGTTCTTGGTTTATTGGACTTGATGTGAATCACATAGATGATCGAAGACTCTGCTGTGGT
|| ||| | | | || || || |||| | | | |||||| |||| | | | | | ||| | | ||||| | | || |||||| |||| | || | |||||| ||||| ||||||||||| |||||||| || ||||| ||||||||||||||||| ||||||| | | || || |||||||| ||| | || |||||
gtaagttttcacttaccattttcaaggggtaaaaaaggaatcagcaaattcttggattgatgtatt--tcataatatcctcttccactttttatggttattt-tgtacatgattattgcagGCATGTTCTTCACAAGTATGCTAATGAGGACGTTTCACTGGGTTCTTGGTTTATTGGTCTTGATGCGGAACATATTGATGATCGGAGATTATGTTGTGGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggtagaaatgttgtgatccacatgattgcttatttgtgtatttctttgtctcagGCACGTTCTCCACAAGTATGCCAATGAGGATGTCTCACTAGGTTCTTGGTTTATTGGACTTGATGTGAATCACATAGATGATCGAAGACTCTGCTGTGGT
tatttctttgtctc CT-rich tract
ttatttgtgtattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtgcttcatctcacttgtggggaaaaaaacaattaaaatcaaatttatggactaaaatggtggtagaaatgttgtgatccacatgattgcttatttgtgtatttctttgtctcagGCACGTTCTCCACAAGTATGCCAATGAGGATGTCTCACTAGGTTCTTGGTTTATTGGACTTGATGTGAATCACATAGATGATCGAAGACTCTGCTGTGGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA