Sequence
atgc intronic sequence ATGC exonic sequence...aatcatttgtacgttgtatatatatccgttaacttttacatctatatatatattccatgttaattaaattggttaatcattgtacacttaactaaaatagGATGTGGATTTAGCTTTACAACAATCAAATGCAAAATGGAAGATTGTGGTGGGTCACCATACAATTAGAAGTGCCGGCGTGCACGGTAATACGGATGAGC
Basic information
species | Glycine max |
transcript | GLYMA08G09880.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G09880.2 (Glycine max), 3'ss of exon 4
lower sequence: AT1G25230.1 (Arabidopsis thaliana), 3'ss of exon 4
aatcatttgtacgttgtatatatatccgttaacttttacatcta--tatatatatt-ccatgttaattaaattggttaatcattgtacacttaactaaaatagGATGTGGATTTAGCTTTACAACAATCAAATGCAAAATGGAAGATTGTGGTGGGTCACCATACAATTAGAAGTGCCGGCGTGCACGGTAATACGGATGAGC
|||| ||| | | | || | | |||| | | || ||| |||| | | || | ||| | ||| ||||| |||| | | | || | |||||| |||||||||||| |||||||||||||||||| | || | ||||| | | || || ||||| | ||||
--------gtac-ttgaaaacacataattaagtcattaccatcagttgtaggaattatcatgatggcgatcccaaatactaatta-gtatttataatgtgtagGAGTTGGAGATGGGTCTAAGAGAATCAAGTGCAAAATGGAAAATTGTGGTGGGTCACCATGCTATAAAGAGTGCTTCCATTCATGGGAATACCAAAGAGC
upper sequence: GLYMA08G09880.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv01s0011g06290.t01 (Vitis vinifera), 3'ss of exon 4
aatcatttgtacgttgtatatatatccgttaacttttacatctatatatatattccatgttaattaaattggttaatcattgtacacttaactaaaatagGATGTGGATTTAGCTTTACAACAATCAAATGCAAAATGGAAGATTGTGGTGGGTCACCATACAATTAGAAGTGCCGGCGTGCACGGTAATACGGATGAGC
| | | | || || || || ||| || || | | ||||||| || || | || | | |||| | | | |||||||||| || ||| | | || | || ||||||||||||||||| || |||||||||||||||||||| || ||||| | || | ||||
-gtaactccatcatttgattaattaataacaatactta--tcaatcca-acgccccatgttgatcaatattcttgactaccaaacacgtttgtgtgacagGATGTGGACACGGCATTAAGAGATTCCACAGCCAAATGGAAGATTGTGGTTGGCCACCATACAATTAGAAGTGCGGGACATCACGGGGACACAGTGGAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatatattccatgttaattaaattggttaatcattgtacacttaactaaaatagGATGTGGATTTAGCTTTACAACAATCAAATGCAAAATGGAAGATTGTGGTGGGTCACCATACAATTAGAAGTGCCGGCGTGCACGGTAATACGGATGAGC
aactaaa putative branch site (score: 2)
ttaattaaattggtta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatcatttgtacgttgtatatatatccgttaacttttacatctatatatatattccatgttaattaaattggttaatcattgtacacttaactaaaatagGATGTGGATTTAGCTTTACAACAATCAAATGCAAAATGGAAGATTGTGGTGGGTCACCATACAATTAGAAGTGCCGGCGTGCACGGTAATACGGATGAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - ccatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtacac