Sequence
atgc intronic sequence ATGC exonic sequence...gtggacatttactcaaaagttactcccattttttaaatggctaccggtaaggcttaaggtgcttcatccattctatatctactttctctacttgtaacagAGTGCTGCTCTAGCTTTGGATGATTCAGTTCTAGACGCTGATCAACTGGAAAATCTCATAAAATTTTGCCCAACAAAAGAGGAGATGGAACTTCTAAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os04g17130.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g17130.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G398731_T01 (Zea mays), 3'ss of exon 2
----gtggacatttactcaaaagttactcccattttttaaatggctaccggtaaggcttaaggtgcttcatccatt-ctatatctactttctctacttgtaacagAGTGCTGCTCTAGCTTTGGATGATTCAGTTCTAGACGCTGATCAACTGGAAAATCTCATAAAATTTTGCCCAACAAAAGAGGAGATGGAACTTCTAAAG
|||| | | ||| ||| |||| || | || |||| || | | |||| | | ||| ||||| |||||||| ||||| |||||||||||||||||||||||||| ||||||||| | || ||||| || | |||||||| ||||||||||||||||||||||||||||||||||||||||||
ttttgtgggaaatctagaaaagattaaccccaaatt---agtgactactagtcaag--taagttttgaagtacatgattatatttactttctgtacttataacagAGTGCTGCTCTAGCTTTGGACGATTCAGTTTTGGATGCTGACCAGATTGAAAATCTAATAAAATTTTGCCCAACAAAAGAGGAGATGGAACTTCTAAAG
upper sequence: LOC_Os04g17130.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA06G21190.1 (Glycine max), 3'ss of exon 9
----gtggacatttactcaaaagttactcccattttttaaatggctaccggtaaggcttaaggtgcttcatccattctatatctactttctctacttgtaacagAGTGCTGCTCTAGCTTTGGATGATTCAGTTCTAGACGCTGATCAACTGGAAAATCTCATAAAATTTTGCCCAACAAAAGAGGAGATGGAACTTCTAAAG
|| || | | | | || || | || |||| || | | || | || | | ||| | || ||| ||| | || ||| ||||||||||||| |||| | |||||| ||||||||||||| |||||||| || || |||||||| || || ||| |||||
ggtaacagattcttgccttatcatatatgtggaaattaaatctcccccctgtaactttttcaatttattgtctttaacatgttgaaattca----tattatcagGCTGCAGTACTGGCTATGGATGATTCAGTGTTAGATGTTGATCAGGTGGAAAATCTCATTAAATTTTGTCCTACCAAAGAGGAAATAGAGCTTTTAAAG
upper sequence: LOC_Os04g17130.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA17G11100.1 (Glycine max), 3'ss of exon 9
--------------------------------------------gtggacatttac-tcaaaagttactcccattttttaaatggctaccggtaaggcttaaggtgcttcatccattctatatctactttctctacttgtaacagAGTGCTGCTCTAGCTTTGGATGATTCAGTTCTAGACGCTGATCAACTGGAAAATCTCATAAAATTTTGCCCAACAAAAGAGGAGATGGAACTTCTAAAG
|| | ||||| | ||| | | || | | |||| | ||||| ||| | | | | | || | || | ||||| || ||| | |||||||||||||| ||||| | || | ||||||| ||||||||||||| || ||||| || || |||||||||||||| ||| | |||
gtaggctgatactttgatgtgggaatctttataatcttgcaagagtagttatttaagttaaaggctgctgatagtagataaacaatcaatggtaaatattatctttcctaacac-tttgaaatggatattctc----------agGCTGCAGTACTAGCTTTGGATGAGTCAGTATTGGATGTTGATCAAGTGGAAAATCTCATTAAGTTTTGTCCTACCAAAGAGGAGATGGATCTTTTGAAG
upper sequence: LOC_Os04g17130.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA05G00820.1 (Glycine max), 3'ss of exon 7
--------------------------------------------------------------------------------------------gtgg-acatttactcaaaagttactcccattttttaaatggctaccggtaaggcttaa-ggt--gcttcatccattctatatctactttctctacttgtaacagAGTGCTGCTCTAGCTTTGGATGATTCAGTTCTAGACGCTGATCAACTGGAAAATCTCATAAAATTTTGCCCAACAAAAGAGGAGATGGAACTTCTAAAG
| | || | || ||| || || | || | |||| | || | || | || ||| | | ||| | ||| | | | | ||| ||| | |||||||||||||| || || | || | ||||||| ||||||||||||| || ||||| || || |||||||||||||| ||| | |||
gtaggctgacacgttgatgtgggcatttttaaaatcatgcaagagtagttatttaagttaaaggctgctgatagtagataaacaatcttttggcaccatatctgctacaaactttttctaacttctgaaatctcaacatggaactatcaatggtaagtattatctttccta-acacgttgaaatggatattctcagGCTGCAGTACTAGCTTTGGATGAGTCGGTATTGGATGTTGATCAAGTGGAAAATCTCATTAAGTTTTGTCCTACCAAAGAGGAGATGGATCTTTTGAAG
upper sequence: LOC_Os04g17130.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT5G07650.1 (Arabidopsis thaliana), 3'ss of exon 3
gtggacatttactcaaaagttactcccattttttaaatggctaccggtaaggcttaaggtgcttcatc----cattctatatctactttctctacttgtaacagAGTGCTGCTCTAGCTTTGGATGATTCAGTTCTAGACGCTGATCAACTGGAAAATCTCATAAAATTTTGCCCAACAAAAGAGGAGATGGAACTTCTAAAG
| | ||| |||| ||| ||| | | | | | |||| | |||| || | || | || | ||||| | | | |||| ||| | || || ||||||| || || |||| | ||||||| | || || || ||||| |||||||||||||| ||||||||||| ||||| |||
---gtaagctac--aaaacctacattaattacctgggtaagaagtcattacgcttcata-gcttaatgataatagtccacattt-ttttctttgcatcgtccagACTGCAGTCCTGGCAATGGATGAGTCTGTAGTAGATGTTGATCAAATAGAGAAACTTATAAAGTTTTGCCCAACAAATGAGGAGATGGAGCTTCTTAAG
upper sequence: LOC_Os04g17130.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT5G07770.2 (Arabidopsis thaliana), 3'ss of exon 6
gtggacatttactcaaaagttactcccattttttaaa--tggctaccggtaaggcttaaggtgcttcatccattctatatctacttt-ctctacttgtaacagAGTGCTGCTCTAGCTTTGGATGATTCAGTTCTAGACGCTGATCAACTGGAAAATCTCATAAAATTTTGCCCAACAAAAGAGGAGATGGAACTTCTAAAG
| | ||| ||| | | | | ||| ||| ||| | ||| |||| || ||| | ||| || | | | ||| ||| | | || ||||||| || || ||||| | ||||||| | || ||||| ||| || ||||||||||||| ||||||||||| ||||| |||
----gtaagctccaaaaccttaattacctgagtaaaagtcaattactggttaatctttcatagcttaatgataattatccacatttttctttgcatcgtccagGCTGCAGTCATGGCAATGGATGAGTCTGTACTAGATGTTGATCAAATAGAGAATCTTATACAACTTTGCCCAACAAAGGAGGAGATGGAGCTTCTTAAG
upper sequence: LOC_Os04g17130.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT5G07740.1 (Arabidopsis thaliana), 3'ss of exon 6
gtggacatttactcaaaagttactcccattttttaaatggctaccggtaaggcttaaggtgcttcatccattctatatctacttt-ctctacttgtaacagAGTGCTGCTCTAGCTTTGGATGATTCAGTTCTAGACGCTGATCAACTGGAAAATCTCATAAAATTTTGCCCAACAAAAGAGGAGATGGAACTTCTAAAG
|| | | |||| | || | || ||| | ||| | || || ||| | ||| || | | | ||| ||| | ||| || ||||||| || || ||||| | ||||||| | || ||||| ||||| ||||||||||| || ||||||||||| || || |||
gtaagttccagtacctactttacctgagtg---aaagtcatgactggttaccctttcatagtttgatgataattattcaaatttttctttgcatcgtccagGCTGCAGTTCTGGCAATGGATGAGTCTGTACTAGATGTTGATCAAATAGAGAATCTTATAAAGTTTTGCCCAACCAAGGAGGAGATGGAGCTACTTAAG
upper sequence: LOC_Os04g17130.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT5G07650.1 (Arabidopsis thaliana), 3'ss of exon 17
gtggacatttactcaaaagttactcccattttttaaatggctaccggtaaggcttaaggtgcttcatccattctatatctactttctctacttgtaacagAGTGCTGCTCTAGCTTTGGATGATTCAGTTCTAGACGCTGATCAACTGGAAAATCTCATAAAATTTTGCCCAACAAAAGAGGAGATGGAACTTCTAAAG
| | | | || || | ||| | | | || |||| | | || || || | || | | | ||| ||| | |||| ||||||| | || ||||| | ||||||| | || ||||| |||| |||||||||||||| ||||||||||| ||||| |||
-------gtaattaagctcctaaacctactttactggttgatgttttatagttttaatga---taatttatcacattattctttgcaccatc-----cagGCTGCAGTACTAGGAATGGATGAGTATGTACTAGATGTTGATCAAATAGAGAATCTTATAAGGTTTTGCCCAACAAAGGAGGAGATGGAGCTTCTTAAG
upper sequence: LOC_Os04g17130.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv17s0000g06640.t01 (Vitis vinifera), 3'ss of exon 8
-gtggacatttactcaaaagttactcccattttttaaatggctaccggtaaggcttaaggtgcttcatccattctatatctactttctctacttgtaacagAGTGCTGCTCTAGCTTTGGATGATTCAGTTCTAGACGCTGATCAACTGGAAAATCTCATAAAATTTTGCCCAACAAAAGAGGAGATGGAACTTCTAAAG
|| || | ||| |||| | || || || ||| || || | | | | |||| | | | ||| ||| | |||||| ||||||| ||| || |||| | ||||||| |||||||||||||||| || ||||| || |||||||||||||||||||| |||
attgctttcttttttgggtccaactatgatttatagtttgattattagttttttttattgttaggcagtagctgt-tgtttactgttgtacatattctcagGCTGCAGTTCTAGCAATGGATGAGTCAATTTTAGATGTTGATCAAGTGGAAAATCTCATAAAGTTCTGCCCTACTAAAGAGGAGATGGAACTTCTTAAG
upper sequence: LOC_Os04g17130.1 (Oryza sativa), 3'ss of exon 8
lower sequence: PP1S246_71V6.1 (Physcomitrella patens), 3'ss of exon 7
-----------------------------------------------gtggacatttactcaaaagttactcccattttttaaatggctaccggtaaggcttaaggtgcttcatccattctatatctactttctctacttgta-acagAGTGCTGCTCTAGCTTTGGATGATTCAGTTCTAGACGCTGATCAACTGGAAAATCTCATAAAATTTTGCCCAACAAAAGAGGAGATGGAACTTCTAAAG
||||| | ||| | | | | || ||||| | || || | | | ||| | ||| | | || |||||| | ||| ||||||| || || | || | |||||| ||||||||||||| || || |||||||| || ||||||||||| | || |
gtaagtgttctaaacattagttttaacttcattcgctgactaggtttcaaaacattcagccaagatgttgcaatactcgtttcttggctcggtggctggttttcccaacattga--gtcttatgttcgcttcttgatatcgtgtgtagAGTGGAGTTCTTTCTTTGGACCCATCTGTATTGGATACAGATCAAGTGGAAAATCTCATTAAGTTCTGCCCAACGAAGGAGGAGATGGATATGCTGAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggtaaggcttaaggtgcttcatccattctatatctactttctctacttgtaacagAGTGCTGCTCTAGCTTTGGATGATTCAGTTCTAGACGCTGATCAACTGGAAAATCTCATAAAATTTTGCCCAACAAAAGAGGAGATGGAACTTCTAAAG
tctactttctctactt CT-rich tract
attctatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtggacatttactcaaaagttactcccattttttaaatggctaccggtaaggcttaaggtgcttcatccattctatatctactttctctacttgtaacagAGTGCTGCTCTAGCTTTGGATGATTCAGTTCTAGACGCTGATCAACTGGAAAATCTCATAAAATTTTGCCCAACAAAAGAGGAGATGGAACTTCTAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - -ctcaaaa
- - - - - - - - - - tactccc
- - - - - - - - - - - - - - - - - - - -gctaccg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgcttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tccattc