Sequence
atgc intronic sequence ATGC exonic sequencegtctgtttcacaatctcttatgcagtggatgttattcacaatatatggctttttatgaggtgatttgtgcactaatggttctaaaactgaaacaacagATATGGAGTTTGGGTTCTCCGGATCCAAATTTCACACTCGATGGACATCAAAAGGGTGTGAACTGTGTTGACTACTTCACTGGTGGTGACAGGCCCTATT
Basic information
species | Oryza sativa |
transcript | LOC_Os06g05180.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 5
gtctgtttc-acaatctcttatgcagtg-gatgttattcacaatatatggctttttatgaggtgatttgtgcactaatggttctaaaactgaaacaacagATATGGAGTTTGGGTTCTCCGGATCCAAATTTCACACTCGATGGACATCAAAAGGGTGTGAACTGTGTTGACTACTTCACTGGTGGTGACAGGCCCTATT
|| | | ||||| | |||| || ||||||| | | | || | ||| | | |||| || | || |||| | |||||| ||||||||||||| |||||||| |||||||| |||||||| |||||||||||||||||||| || |||||||||||||||||||||||||||||||||||||
gtgcgccttgacaatat--tatggagcaagatgttagttgcgac---tgagtcaagatgtgat--cttgttcattcatacttctcactctgaaattgtagATATGGAGTTTAGGTTCTCCAGATCCAAACTTCACACTTGATGGACATCAAAAGGGTGTCAATTGTGTTGACTACTTCACTGGTGGTGACAGGCCCTATT
upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G000645_T03 (Zea mays), 3'ss of exon 6
----gtctgtttcacaatctcttatgcagtg-gatgttattcacaatatatggctttttatgaggtgat-ttgtgcactaatggttctaaaactgaaacaacagATATGGAGTTTGGGTTCTCCGGATCCAAATTTCACACTCGATGGACATCAAAAGGGTGTGAACTGTGTTGACTACTTCACTGGTGGTGACAGGCCCTATT
| || ||| |||| | ||||||| | ||||||| | | | |||| ||||| |||| || | || |||| | |||| | ||||||||||||||||||||||| |||||||| |||||||| ||||| |||||||||||||| ||||||||||||||||||||||||||||||||||||||||
gtatgcct-ttttgcaatat--tatgcagcgagatgttaactgcgac----------tcatgatgtgatcttgttcatttatacttcttactttgaa-ctgcagATATGGAGTTTGGGTTCTCCAGATCCAAACTTCACACTTGATGGGCATCAAAAGGGTGTCAACTGTGTTGACTACTTCACTGGTGGTGACAGGCCCTATT
upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G419984_T01 (Zea mays), 3'ss of exon 5
----gtctgtttcacaatctcttatgcagtg-gatgttattcacaatatatggctttttatgaggtgat-ttgtgcactaatggttctaaaactgaaacaacagATATGGAGTTTGGGTTCTCCGGATCCAAATTTCACACTCGATGGACATCAAAAGGGTGTGAACTGTGTTGACTACTTCACTGGTGGTGACAGGCCCTATT
| || ||| |||| | ||||||| | ||||||| | | | |||| ||||| |||| || | || |||| | |||| | ||||||||||||||||||||||| |||||||| |||||||| ||||| |||||||||||||| |||||||||||||||||||||||||||||||| |||||||
gtatgcct-ttttgcaatat--tatgcagcgagatgttaactgcgac----------tcatgatgtgatcttgttcatttatacttcttactttgaa-ctgcagATATGGAGTTTGGGTTCTCCAGATCCAAACTTCACACTTGATGGGCATCAAAAGGGTGTCAACTGTGTTGACTACTTCACTGGTGGTGACAGACCCTATT
upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 6
gtctgtttcacaatctcttatgcagtggatgttatt-cacaatatatggctttt---tatgaggtgatttgtgcactaatggttctaaaac-tgaaacaacagATATGGAGTTTGGGTTCTCCGGATCCAAATTTCACACTCGATGGACATCAAAAGGGTGTGAACTGTGTTGACTACTTCACTGGTGGTGACAGGCCCTATT
| | || | | || || | | || | || ||| | | | | ||| ||| | | | |||||| | | | | ||||| |||| | | || || || || |||||||| || | |||| || || || || ||||||||||| ||||||||||||||||||| ||| || |
-tatacttta-agtcgctgttttggcggctttttcaatacagtttttctcctttacttataaaa-aaaaaaagtcctaatgttgatctggcgtcctgttccagATTTGGAATCTCGGCTCCCCTGACCCAAATTTTACTTTGGATGACCACATGAAAGGGGTAAACTGTGTTGATTACTTCACTGGTGGTGACAAGCCATACT
upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 6
lower sequence: PP1S243_63V6.1 (Physcomitrella patens), 3'ss of exon 6
-------------------------------------------------------------------------------------------gtctgtttcacaatctcttatgcagtggatgttattcacaatatatggctttttatgaggtgatttgtgcactaatggttctaaaactgaaacaacagATATGGAGTTTGGGTTCTCCGGATCCAAATTTCACACTCGATGGACATCAAAAGGGTGTGAACTGTGTTGACTACTTCACTGGTGGTGACAGGCCCTATT
|||| ||| || | | |||| | || ||||| || | | |||| |||| | | | ||| || | ||||||||| |||||||| || || || || || || ||||| | ||||| |||||||| ||||| || || |||||||||||||||||| | || |||
gtgagatattatgtgcttcgatgttcttctattggcattatgtacgtaaagaaattctatgaaaaaaaaaggaagagttttaatccactcgacttgttgtggaatgcttttttagggtagtgttctaaacg-tatatcgccatat-tgagttgatcag------atgagctctgtctttgta----tagATATGGAACTTGGGTTCACCAGAGCCCAACTTTACCCTCGAGGCTCATCAGAAGGGTGTCAACTGCGTGGAATACTTCACTGGTGGTGACCGACCACATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatggctttttatgaggtgatttgtgcactaatggttctaaaactgaaacaacagATATGGAGTTTGGGTTCTCCGGATCCAAATTTCACACTCGATGGACATCAAAAGGGTGTGAACTGTGTTGACTACTTCACTGGTGGTGACAGGCCCTATT
ttctaaa putative branch site (score: 2)
tttttatga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctgtttcacaatctcttatgcagtggatgttattcacaatatatggctttttatgaggtgatttgtgcactaatggttctaaaactgaaacaacagATATGGAGTTTGGGTTCTCCGGATCCAAATTTCACACTCGATGGACATCAAAAGGGTGTGAACTGTGTTGACTACTTCACTGGTGGTGACAGGCCCTATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG