Sequence
atgc intronic sequence ATGC exonic sequence...ttggccagctactagctagtagtagcagctattgtaactttgcatcgtttggaacattttaaggtgaatgatgcagagagtttgttcgatgattttacagGTGGCTATGATAAGGAGGAGAAAGCGGCGAGGGCGTATGATCTTGCCGCGTTGAAGTACTGGGGTCCTAGCACCACAACCAACTTTCCG
Basic information
species | Oryza sativa |
transcript | LOC_Os04g55970.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g55970.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G086573_T01 (Zea mays), 3'ss of exon 4
------------ttggccagctactagctagtagtagcagctattgtaactttgcatcgtttggaa-cattttaaggtgaatgatgcagagagtttgttcgatgattttacagGTGGCTATGATAAGGAGGAGAAAGCGGCGAGGGCGTATGATCTTGCCGCGTTGAAGTACTGGGGTCCTAGCACCACAACCAACTTTCCG
| | |||| | | | | | | | || | | | | | || ||| ||| | | ||| | | | ||| || |||| | | |||||||||||||||||||||||| || || ||||||||||||||||| || ||||||||||||||| |||||||||| ||||||||||||
gtaagaactgattaaacaagcttcatgtttatttcattatccat-gcatcatctcgtcaagcagaagcatcacattgctgatggtact---attttttttcatgaatctgaagGTGGCTATGATAAGGAGGAGAAGGCTGCCAGGGCGTATGATCTTGCAGCTTTGAAGTACTGGGGTTCTAGCACCACCACCAACTTTCCG
upper sequence: LOC_Os04g55970.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv11s0052g00840.t01 (Vitis vinifera), 3'ss of exon 4
-------------------------------------ttggccagctactagctagtagtagcagctattgtaactttgcatcgtttggaa---cattttaaggtgaatgatgcagaga-gtttgttcgatgattttacagGTGGCTATGATAAGGAGGAGAAAGCGGCGAGGGCGTATGATCTTGCCGCGTTGAAGTACTGGGGTCCTAGCACCACAACCAACTTTCCG
|| ||| | || || || | | ||| | ||| || |||||| | | | | ||| || || ||| ||||||| ||||||||||| ||||| || || || || |||||||| ||||| | |||||||||||||| | |||||| || ||||| ||
gtgagtaggatctcatctcgtggtcttgtcctgaatcatgatttttcactgttgaataaaagattctgatattccttcaagt--tttagattctcattttggatcaatttttatttatttatttattttttg--tttgcagGTGGGTATGATAAGGAAGAGAAGGCAGCTAGAGCTTATGATCTCGCCGCTCTTAAGTACTGGGGTCCGACCACCACCACTAACTTCCCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgtttggaacattttaaggtgaatgatgcagagagtttgttcgatgattttacagGTGGCTATGATAAGGAGGAGAAAGCGGCGAGGGCGTATGATCTTGCCGCGTTGAAGTACTGGGGTCCTAGCACCACAACCAACTTTCCG
aacattttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttggccagctactagctagtagtagcagctattgtaactttgcatcgtttggaacattttaaggtgaatgatgcagagagtttgttcgatgattttacagGTGGCTATGATAAGGAGGAGAAAGCGGCGAGGGCGTATGATCTTGCCGCGTTGAAGTACTGGGGTCCTAGCACCACAACCAACTTTCCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - -cagctac
- - - - - - - - - - - tagcagc
- - - - - - - - - - - - - - - - - - -ctttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgca