Sequence
atgc intronic sequence ATGC exonic sequencegtgcatgatcattttgagcattatatttcgctaattttgcttcttttttactgattattatttgctaattgcttctacagCTCCAGAAGATAAAATCTGAAATATCTGAAGTGTCTGGTGATCCACATGGTCTACTTATGGAAGCGCTCCATTCGGCTGGATATTCTGGGGCTCTGGCAA
Basic information
species | Oryza sativa |
transcript | LOC_Os05g44916.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g44916.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G005036_T01 (Zea mays), 3'ss of exon 3
gtgcatgatcattttgagcattatatttcgctaattttgcttcttttttactgattattatttgctaattgcttctacagCTCCAGAAGATAAAATCTGAAATATCTGAAGTGTCTGGTGATCCACATGGTCTACTTATGGAAGCGCTCCATTCGGCTGGATATTCTGGGGCTCTGGCAA
|| | | |||| | || || | | | | |||| ||||| | || | | | | | |||||||||||||||| ||||||||||||||| |||| | ||||| | |||| || ||||||||| |||| || || ||||||| ||||||||| ||||| |||||||
gtactttatcact--gaaaataaattgaagttctttttttcatccttttatgtactaatggc-gttcttcgtttctacagCTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGTCTACTTCTGGAGGCCCTTCATTCGGTTGGATATTCCGGGGCACTGGCAA
upper sequence: LOC_Os05g44916.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G447379_T01 (Zea mays), 3'ss of exon 1
------------gtgcatgatcattttgagcattatatttcgctaattttgcttcttttttactgattattatttgctaattgcttctacagCTCCAGAAGATAAAATCTGAAATATCTGAAGTGTCTGGTGATCCACATGGTCTACTTATGGAAGCGCTCCATTCGGCTGGATATTCTGGGGCTCTGGCAA
| | | |||| | || || | || | | |||| | || |||| | | || | | || | | |||||||||||||||| ||||||||||||||| |||| |||| | | |||| || | ||||||| |||| || || ||||||| ||||||||| ||||| ||| |||
gtcaaagagcagatactttatcact--gaaaataaatttaagttcttttttcatccttttatgtactaatggtgttct--tcgtttctacagCTCCAGAACATAAAATCTGAAATAGCTGATGTGTTCGCTAATCCTCAAGATCTACTTCTGGAGGCCCTTCATTCGGTTGGATATTCCGGGGCACTGACAA
upper sequence: LOC_Os05g44916.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G068336_T01 (Zea mays), 3'ss of exon 3
gtgcatgatcattttgagcattatatttcgctaattttgcttcttttttactgattattatttgctaattgcttctacagCTCCAGAAGATAAAATCTGAAATATCTGAAGTGTCTGGTGATCCACATGGTCTACTTATGGAAGCGCTCCATTCGGCTGGATATTCTGGGGCTCTGGCAA
|| | | |||| | || || | || | | |||| ||||| | || | | | | | |||||||||||||||| ||||||||||||||| |||| ||||||| | |||| || ||||||||| | || || || ||||||| ||||||||||||||| |||||||
gtactttatcact--gaaaataaatttaagttctttttttcatccttttatgtactaatggt-gttcttcatttctacagCTCCAGAACATAAAATCTGAAATAGCTGATGTGTCTGCTAATCCTCAAGGTCTACTTTTAGAGGCCCTTCATTCGGTTGGATATTCTGGGGCACTGGCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttcgctaattttgcttcttttttactgattattatttgctaattgcttctacagCTCCAGAAGATAAAATCTGAAATATCTGAAGTGTCTGGTGATCCACATGGTCTACTTATGGAAGCGCTCCATTCGGCTGGATATTCTGGGGCTCTGGCAA
tgctaat putative branch site (score: 2)
ttgcttct CT-rich tract
ttttttactgattatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcatgatcattttgagcattatatttcgctaattttgcttcttttttactgattattatttgctaattgcttctacagCTCCAGAAGATAAAATCTGAAATATCTGAAGTGTCTGGTGATCCACATGGTCTACTTATGGAAGCGCTCCATTCGGCTGGATATTCTGGGGCTCTGGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA