Sequence
atgc intronic sequence ATGC exonic sequencegtatgaccgtttcttttaggatctgtgctgggttccataatattgccatcctgtgataacttgtaatcttggtattttagGTTGGAAATCAAACAGGCAAGTGAAGGGTCCCATCATGTCCCTGGCATTGTGGAGGCCAAAGTTGAGAACATCAAGGAGGTTTGGGATGTCTTGCAAGCT
Basic information
species | Oryza sativa |
transcript | LOC_Os03g02290.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g02290.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G092232_T01 (Zea mays), 3'ss of exon 8
gtatgaccgtttctttt-aggatctgtgctgggttccataatattgccatcctgtgataacttgtaatcttggtatt----ttagGTTGGAAATCAAACAGGCAAGTGAAGGGTCCCATCATGTCCCTGGCATTGTGGAGGCCAAAGTTGAGAACATCAAGGAGGTTTGGGATGTCTTGCAAGCT
||| | || | || ||| ||| | | || || | | | ||| ||||| || || || ||||| |||| ||||| | |||||||| ||||||||||||| | |||||||||||| |||||||||| || ||||||||| | || |||||| ||
gtacaaaaaattatcttcaggtcctgattttttgtttgtagtagtaggagctcgtgttaactcaacattcacgttttgcatttagGCTGGAGATCAAGCCAAACAGTGAAGGACAAAATCATGTCCCTGGGTTAGTGGAGGCCAAAATTGAGAACATAAATGAGGTTTGGAAAGTTTTGCAAACT
upper sequence: LOC_Os03g02290.2 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv18s0001g07800.t01 (Vitis vinifera), 3'ss of exon 8
--------------------------------------------------------------------------------------------------------------gtatgaccgt-----ttcttttaggatctgtgctgggttccataatattgccatcctgtgat--aacttgtaat-cttggtattttagGTTGGAAATCAAACAGGCAAGTGAAGGGTCCCATCATGTCCCTGGCATTGTGGAGGCCAAAGTTGAGAACATCAAGGAGGTTTGGGATGTCTTGCAAGCT
|| | | | | | || | | | | ||| || | | | | | || || ||| | | ||| || ||||||| || || | || |||| ||||||| ||||||||| || || |||||||| ||||||||||||||||| |||||||| |||||||| ||||||||
gtaaaattattatttactcatattctcagcattcttttgaaaaacaaaggggaaattttttttcaactgagacactatttttgttcttagccaatgaatttgacttggttaaataatcataaaaatgccttcatgttattggctcattttgactagccaacaaactgtcaattgaatttgaatttctttcaatgttagGTTAGAGATAAGGCAAGCAACTGAAGGGGTCCATCATGTACCAGGGATTGTGGAAGCCAAAGTTGAGAACATTAAGGAGGTCTGGGATGTTCTGCAAGCT
upper sequence: LOC_Os03g02290.2 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv00s0218g00050.t01 (Vitis vinifera), 3'ss of exon 10
-------------------------------------------------------------------------------------gtatgaccgtttcttttaggatctgtgctgggttccataatattgcca--------tcctgtgataacttgtaatcttggt--attttagGTTGGAAATCAAACAGGCAAGTGAAGGGTCCCATCATGTCCCTGGCATTGTGGAGGCCAAAGTTGAGAACATCAAGGAGGTTTGGGATGTCTTGCAAGCT
| | | ||| || |||||| | | || |||| | | ||| || | ||| ||| || ||||||||| || || || | |||||| | ||||||||||| || ||||||||||||||||| |||||||| || || || ||| | ||| |||| |||
gtaaaattgtgcttcattgattattttaagaatcccaacctagccagcaaacctttgaaaacatactggagttcacagccttttgaactcagtaggttagaagggaagtgggctgggctgaaaaaaattgatgaatgtaagtagcctattaattttttatcctggatgatgctagGTTGGAGATAAAGCAATCTTCTGAAGGTTTTCATCATGTCCCGGGGATTGTGGAGGCCAAAGTGGAGAACATTAAAGAAGTCTGGAAAGTCCTGCAGGCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgctgggttccataatattgccatcctgtgataacttgtaatcttggtattttagGTTGGAAATCAAACAGGCAAGTGAAGGGTCCCATCATGTCCCTGGCATTGTGGAGGCCAAAGTTGAGAACATCAAGGAGGTTTGGGATGTCTTGCAAGCT
tgataac putative branch site (score: 2)
ataatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgaccgtttcttttaggatctgtgctgggttccataatattgccatcctgtgataacttgtaatcttggtattttagGTTGGAAATCAAACAGGCAAGTGAAGGGTCCCATCATGTCCCTGGCATTGTGGAGGCCAAAGTTGAGAACATCAAGGAGGTTTGGGATGTCTTGCAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT