Sequence
atgc intronic sequence ATGC exonic sequence...aattctttctcctattttctgttcaatttcatttaatcactagtattaatctttggttattaacacatgctcacttttttccttgttgatctatttacagAAAAGTCCCAGATAGGCCCAGAGATCCTGCTAAGTGGAATGAAATCGCTGATGTTGTGTCAGCATTATCTATTCCAGTTATAGAAAATGGTGATGTTTTT
Basic information
species | Glycine max |
transcript | GLYMA08G36840.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G36840.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os04g44890.1 (Oryza sativa), 3'ss of exon 5
---aattctttctcctattttctgttcaatttcatttaatcactagtattaatctttggttattaacacatgctcacttttttccttgttgatctatttacagAAAAGTCCCAGATAGGCCCAGAGATCCTGCTAAGTGGAATGAAATCGCTGATGTTGTGTCAGCATTATCTATTCCAGTTATAGAAAATGGTGATGTTTTT
||| | || ||| || | || ||||| | || ||| ||| ||||| || |||| || | | || | | | | |||||| ||| ||| || || |||||||||||||||||| |||| || || ||||||||||| ||| | || ||||||||||||| ||||| ||||| |||
cagaataatgtcatatatcaactctccattttcaatct-tccctaatat--gtctttttttgttaattgatttccctgatgttggattcctttacacatgcagAAAGGTCAAAGACAGACCAAGAGATCCTGCTAAGTGGGATGAGATTGCAGATGTTGTGTCTGCACTGTCAATTCCAGTTATAGCTAATGGAGATGTATTT
upper sequence: GLYMA08G36840.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G468693_T03 (Zea mays), 3'ss of exon 2
--------------------------------------------------------------------------------aattctttctcctattttc--tgttcaatttcattta-atcactagtattaatctttggt-tattaacacatgctcacttttttccttgttgatctattt-------acagAAAAGTCCCAGATAGGCCCAGAGATCCTGCTAAGTGGAATGAAATCGCTGATGTTGTGTCAGCATTATCTATTCCAGTTATAGAAAATGGTGATGTTTTT
|| | | |||| | | | ||||||| | | ||| | ||| | || || || | | |||| ||||| || || |||||| | |||||| || ||||||| ||| |||||| |||| || ||||||||||||||||| | || ||||||||||||| ||||| ||||| |||
gtaatgacacatagaattgtatttttgagttgtgatagtctggtagataattgaaaccattcttactctagctttagaagcatgcaattagctatctgcatttttcaattatgtcaatatctccctcattttttttgagtacgcccttttataattagttttgcttatgttgctcctctttgaaatcgcagAAAGATTAAAGATAGACCGAGAGATCTTGCCAAGTGGGATGAGATAGCTGATGTTGTGTCAGCGCTGTCAATTCCAGTTATAGCTAATGGAGATGTCTTT
upper sequence: GLYMA08G36840.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G49640.2 (Arabidopsis thaliana), 3'ss of exon 5
--aattctttctcctattttctgttcaatttcatttaatcactagtattaatctttggttattaacacatgctcacttttttccttgttgatctatttacagAAAAGTCCCAGATAGGCCCAGAGATCCTGCTAAGTGGAATGAAATCGCTGATGTTGTGTCAGCATTATCTATTCCAGTTATAGAAAATGGTGATGTTTTT
||| | || || | ||| | ||||| |||| || | | || || | | || ||||| || | | ||||| ||| | |||| ||||| |||||||||||||| ||| |||| || || ||||| ||| |||||||||| ||||| || || | |||||| ||||||||
gtaatatacaccactgttgttagtttgttctcattc---------ctttaagctgttttaatcaaagttgg--taattgattcctccttccttaaaatacagGAAAATTGCAGACAGGCCAAGAGATCCTGCTAAATGGGATGAGATTGCAGATGTGGTGGCAGCATTATCCATTCCCGTCATTGCAAATGGCGATGTTTTA
upper sequence: GLYMA08G36840.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv00s2201g00010.t01 (Vitis vinifera), 3'ss of exon 3
aattctttctcctattttctgttcaatttcat--ttaatcactagtattaatctttgg--ttattaacacatgctcacttttttccttgttgatctatttacagAAAAGTCCCAGATAGGCCCAGAGATCCTGCTAAGTGGAATGAAATCGCTGATGTTGTGTCAGCATTATCTATTCCAGTTATAGAAAATGGTGATGTTTTT
| || | | | |||| | || || || |||| ||| | |||| | |||| | | | || || | || ||||| | | |||||||||| || |||||||||||||||||||| || ||||||||||| | |||||||||||||| ||||||| |||||||||||| |||
---ttttattttaaaaaaataaaaaattatacaattgatt-ttattatttccttttaaactgcataactagttgtcacatgcattcctgatggatgaattgcagAAGAATTGCAGATAGGCCTAGGGATCCTGCTAAGTGGAATGAGATTGCTGATGTTGTAGCGGCATTATCTATTCCGGTTATAGCAAATGGTGATGTCTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaatctttggttattaacacatgctcacttttttccttgttgatctatttacagAAAAGTCCCAGATAGGCCCAGAGATCCTGCTAAGTGGAATGAAATCGCTGATGTTGTGTCAGCATTATCTATTCCAGTTATAGAAAATGGTGATGTTTTT
tctattt CT-rich tract
ttattaaca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aattctttctcctattttctgttcaatttcatttaatcactagtattaatctttggttattaacacatgctcacttttttccttgttgatctatttacagAAAAGTCCCAGATAGGCCCAGAGATCCTGCTAAGTGGAATGAAATCGCTGATGTTGTGTCAGCATTATCTATTCCAGTTATAGAAAATGGTGATGTTTTT
- - - - - - - - ttctgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacacat