Sequence
atgc intronic sequence ATGC exonic sequence...tacaatacctaaaaccctagcttttcatttcctgattttctctcctaccagctgcaagattaggaaaactaaccatgtttgcaacccctggtttatgcagATGTTCAAACTAGAAGATGTAGCAATGGGTATATGGATTGCTGAAATGAAGAAGGGTGGGTTACCTGTCCAATACAAAACAGATGAAAGAATTAACAGTG
Basic information
| species | Oryza sativa |
| transcript | LOC_Os02g36770.1 |
| intron # | 8 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g36770.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AC206332.3_FGT005 (Zea mays), 3'ss of exon 4
tacaatacctaaaaccctagcttttcatttcctgattttctctcctacc-----agctgcaagattaggaaaactaaccatgtttgcaacccctggtttatgcagATGTTCAAACTAGAAGATGTAGCAATGGGTATATGGATTGCTGAAATGAAGAAGGGTGGGTTACCTGTCCAATACAAAACAGATGAAAGAATTAACAGTG
| |||| | |||||| |||| | || ||| | || | || || | | | | | | || | | ||| ||||||||||||||||| |||||||||||||| |||||| | |||||||||||| ||||| ||||| || |||| ||||||| | |||||||||| |
----tcaactaatagt-tagcttgtcatctgatgtgtttgacatctgcttcggaagatggtaatcagattagaagagctaaattagatgctatgacttttcacagATGTTCAAACTAGAGGATGTAGCAATGGGCATATGGGTAAATGAAATGAAGAAAGGTGGATTACCAGTGAAATATGAAACAGACAAGAGAATTAACATCG
upper sequence: LOC_Os02g36770.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA01G05860.1 (Glycine max), 3'ss of exon 7
tacaatacctaaaaccctagcttttcatttcctgattttctctcctac-cagctgcaa-gattaggaaaactaaccatgtttg---caacccctggtttat---gcagATGTTCAAACTAGAAGATGTAGCAATGGGTATATGGATTGCTGAAATGAAGAAGGGTGGGTTACCTGTCCAATACAAAACAGATGAAAGAATTAACAGTG
|| | || | | || | || | | || | || || | || |||| ||| | || ||| | | | ||||||||| ||||||||||| || |||||||| || ||||| ||||| |||||||||| || || || | || | | || | ||| | || ||
--------ctccatttttacatgggaaattggaaaactttcgttcaacatggttggaacggttttccaaacacaccctcaatgattcaatgttaactctttctggcagATGTTTAAACTAGAAGACGTTGCAATGGGAATCTGGATCGCTGACATGAAGAAGGAAGGTCTAGAAGTTCGCTATGAGAATGAGGTCAGAGTGTACCCTG
upper sequence: LOC_Os02g36770.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA02G12030.1 (Glycine max), 3'ss of exon 6
------------------------------------------------------------------------tacaatacctaaaaccctagcttttcatttcctgattttctctcctaccagctgcaagat-------taggaaaactaaccatgtttgcaaccc--ctggtttatgcagATGTTCAAACTAGAAGATGTAGCAATGGGTATATGGATTGCTGAAATGAAGAAGGGTGGGTTACCTGTCCAATACAAAACAGATGAAAGAATTAACAGTG
||| | | | | | | |||| | | || | | || | | | || | ||| || | || ||| ||||||||| ||||||||||| || |||||||| || ||||| || || |||||||||| || || || | || | | || ||| | | |
gtatataataaaatccattatttgttgaaaactgtttgtatagttgctatagtgctaaatgtgttttgtgcaaacactgttgacatctttgaacgccaagcaagctcccttctgttcaacgtggtttaaaacggttttccaaacacaccctcaatgattcaattttaactctttttggcagATGTTTAAACTAGAAGACGTTGCAATGGGAATCTGGATCGCAGACATGAAGAAGGAAGGTCTAGAAGTTCGCTATGAGAATGAGATCAGAGTCTATCCCG
upper sequence: LOC_Os02g36770.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT1G26810.1 (Arabidopsis thaliana), 3'ss of exon 7
tacaatacc-taaaaccctagcttttcatttcctgattttctctcctaccagctgcaagattaggaaaactaaccatgtttgcaacccctggtttatgcagATGTTCAAACTAGAAGATGTAGCAATGGGTATATGGATTGCTGAAATGAAGAAGGGTGGGTTACCTGTCCAATACAAAACAGATGAAAGAATTAACAGTG
|| || || ||| | | || | ||| | || | | | | | || |||| || || | ||||||| || ||||||||||| |||||||| |||||||| ||||| ||| || ||| | || ||| ||| |||| ||| || | ||||
----gtattgtactactctatgctaactccattcaatcacatttccgg--attcacatagaaatggattgtgaaaatttttgaaatttgtgaat-----agATGTTTAAGCTAGAAGATGTGGCAATGGGGATATGGATAGCTGAGCTGACAAAACATGGACTCGAGCCTCATTACGAAAACGATGGAAGGATCATTAGTG
upper sequence: LOC_Os02g36770.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv14s0108g00890.t01 (Vitis vinifera), 3'ss of exon 6
--tacaatacctaaaaccctagcttttcatttcctgattttctctcctaccagctgcaagattaggaaaactaaccatgtttgcaacccctggtttatgcagATGTTCAAACTAGAAGATGTAGCAATGGGTATATGGATTGCTGAAATGAAGAAGGGTGGGTTACCTGTCCAATACAAAACAGATGAAAGAATTAACAGTG
|| |||| | |||| ||| | | || | | || | | | || | | || | | | | ||||||||||||| || ||||||||||||||||| || ||||| || || ||||||||||| || | || |||| || ||| || || | | | ||
atagtgatgattaaataagaattttttaattgttcaaagtactaaatggcatgttggtgaacca--acaattttgcttgacaacgagattatatgtgtgcagATGTTCAAGCTGGAAGATGTAGCAATGGGGATCTGGATAGCAGAGATGAAGAAGGGGGGAATGGAGGTTAGTTACATAAAAGAAGAGAGGGTCTATAATG
upper sequence: LOC_Os02g36770.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv01s0026g02530.t01 (Vitis vinifera), 3'ss of exon 6
-------------------------------------------------------------------------------------------------tacaat--acctaaaaccctagcttttcatttcctgattttc---tctcctaccagct-gcaagattaggaaaactaaccatgtttgcaacccctggtttatgcagATGTTCAAACTAGAAGATGTAGCAATGGGTATATGGATTGCTGAAATGAAGAAGGGTGGGTTACCTGTCCAATACAAAACAGATGAAAGAATTAACAGTG
||||| | |||| | | | | || | | | | || | ||| | | || || |||| || | || || | | || | | |||||||||| || || |||||||| || ||||| || |||||||| || ||||||||||| || | || || | | || ||||| | | | ||
gtataatagtcactgatcttgctttttcccttccaatcataaaccatttttgacagtctacaattgcagcactggtctgaacaggaagtcctttgccaacaatgaagctaatttctatggatattggctcttaaatcacatatcacatacaggttcacacatttttgaaatctgaaaatatt---agttcttgatat-tgcagATGTTTAAGCTTGAAGATGTGGCGATGGGCATCTGGATTGCAGATATGAAGAAGGGAGGTATGGAAGTTTGGTATGAGAAGGAAGAAAGGGTCTATAATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taccagctgcaagattaggaaaactaaccatgtttgcaacccctggtttatgcagATGTTCAAACTAGAAGATGTAGCAATGGGTATATGGATTGCTGAAATGAAGAAGGGTGGGTTACCTGTCCAATACAAAACAGATGAAAGAATTAACAGTG
aactaac putative branch site (score: 1)
aaaactaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tacaatacctaaaaccctagcttttcatttcctgattttctctcctaccagctgcaagattaggaaaactaaccatgtttgcaacccctggtttatgcagATGTTCAAACTAGAAGATGTAGCAATGGGTATATGGATTGCTGAAATGAAGAAGGGTGGGTTACCTGTCCAATACAAAACAGATGAAAGAATTAACAGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - acctaaa
- - - - - - - - - - - tttcatt
- - - - - - - - - - - - - - - - - - - - - - - - -agctgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaactaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttgc
