Sequence
atgc intronic sequence ATGC exonic sequence...tgatgttgccaatgatcaatatcaatgtataccatattcatttgtattgttcgtgcaatatattttattatgtttcatttaatgtgtttgctttatgcagTATATCTTCATCAGACCTTGTTTCAAAATGGATGGGAGAGAGTGAAAAACTTGTTGCAAACCTTTTCCAAATGGCTCGAGAAAACGCTCCTTCCATTATC
Basic information
species | Oryza sativa |
transcript | LOC_Os01g04814.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g04814.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G088834_T01 (Zea mays), 3'ss of exon 2
tgatgttgccaatgatcaat--atcaatgtataccatattcat-ttgtattgttcgtgcaatatattttat-tatgtttcatttaatgtgtttgcttta-tgcagTATATCTTCATCAGACCTTGTTTCAAAATGGATGGGAGAGAGTGAAAAACTTGTTGCAAACCTTTTCCAAATGGCTCGAGAAAACGCTCCTTCCATTATC
|| | |||| | || |||| | ||| | || | || || || ||| ||| | | | |||| | |||||||| |||||||||||||| ||||| || |||||||| |||||||| || ||||| ||| | |||||||| || |||||||||||||| ||||| || ||||||||||||
-----tttcacttgattggtcaatggatgttagcaatactaatatcctaccatttgttttctatgccgtatctttatgatatttcacactgttgctttactgcagTATATCTTCTTCAGATCTGGTTTCAAAGTGGATGGGTGAAAGTGAGAAATTAGTTGCAAATCTGTTCCAAATGGCTCGGGAAAATGCCCCTTCCATTATC
upper sequence: LOC_Os01g04814.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G126860_T01 (Zea mays), 3'ss of exon 2
tgatgttgccaatgatcaatatcaatgtataccatattcatttgtattgttcgtgcaa-tatattttattatgtttcatttaatgtgtttgctttat-gcagTATATCTTCATCAGACCTTGTTTCAAAATGGATGGGAGAGAGTGAAAAACTTGTTGCAAACCTTTTCCAAATGGCTCGAGAAAACGCTCCTTCCATTATC
|| | | || | | |||| ||| | | | | | |||| ||| || | |||| | ||||||||| ||||||||||||| ||||| || |||||||| |||||||| || || || ||| | || ||||| ||||||||||||||||| ||||| || ||||||||||||
--atctaacttgcaattttttagtttacatacttgattggtcaatgtaagataccctactatactttttttcatgatatttcacaatgttgctttattgcagTATATCTTCTTCAGATCTGGTTTCAAAGTGGATGGGTGAAAGCGAGAAATTAGTCGCAAATCTTTTCCAAATGGCTCGTGAAAATGCCCCTTCCATTATC
upper sequence: LOC_Os01g04814.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA11G19120.1 (Glycine max), 3'ss of exon 2
---tgatgttgccaatgatcaatatcaatgtataccatattcatttgtattgtt-cgtgcaatatattttattatgtttcatttaatgtgtttgctttatgcagTATATCTTCATCAGACCTTGTTTCAAAATGGATGGGAGAGAGTGAAAAACTTGTTGCAAACCTTTTCCAAATGGCTCGAGAAAACGCTCCTTCCATTATC
||| || || | | || || | | | || | | | ||| | | || | |||||| | | || || ||| | |||| | |||||||||||||| |||||||| ||||||||||| |||||||| || || |||| ||||||||||||||||| |||| || ||||| || ||
ccttgacagtgattttgtttgaaataaa-aaaggttgtgaatgtgagtgctttggtgggcattttcttgcagcatgttttaacttttgaatt--cttcac-cagTGTTTCTTCATCAGACCTGGTTTCAAAGTGGATGGGAGAAAGTGAAAAGCTGGTCTCAAATCTTTTCCAAATGGCTCGCGAAAGTGCACCTTCTATAATA
upper sequence: LOC_Os01g04814.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA12G09300.1 (Glycine max), 3'ss of exon 2
------tgatgttgccaatgatcaatatcaatgtataccatattcatttgtattgttcgtgcaatatattttattatgtttcatttaatgtgtttgctttatgcagTATATCTTCATCAGACCTTGTTTCAAAATGGATGGGAGAGAGTGAAAAACTTGTTGCAAACCTTTTCCAAATGGCTCGAGAAAACGCTCCTTCCATTATC
|||| ||| ||| |||| | | | || || || | ||| | | || |||||| | | | || ||| | |||| | ||||| |||||||| |||||||| ||||||||||| |||||||| || || |||| |||||||||||||| || |||| || ||||| || ||
tgtcagtgattttgtt--tgaaaaataaggtcgcaaat-gtaagtgcttaggttaggtgggcatttttttgctacatgttttaactttttaatt--cttcac-cagTGTTTCTTCGTCAGACCTGGTTTCAAAGTGGATGGGAGAAAGTGAAAAGCTGGTCTCAAATCTTTTCCAAATGGCACGCGAAAGTGCACCTTCTATCATA
upper sequence: LOC_Os01g04814.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA13G39410.1 (Glycine max), 3'ss of exon 2
--tgatgttgccaatgatcaatatcaatgtataccatattcatttgtattgttcgtgcaatatattttattatgtttcatttaatgt-gtttgctttatgcagTATATCTTCATCAGACCTTGTTTCAAAATGGATGGGAGAGAGTGAAAAACTTGTTGCAAACCTTTTCCAAATGGCTCGAGAAAACGCTCCTTCCATTATC
| | | | ||| || || || || | || | ||| | || || | | | | || | | | | | ||| || |||| | ||||||||||||||||||||||| |||||||| || |||||||| || ||| ||||||||||| ||||||||||||||| || ||||| || ||
ccttaaatcaggtaaattcatattccataaatgttatgaatgtaggt-ccataagtg-gacatgttcttgcaagcatttttaacttttgaattcttcat-cagTGTTTCTTCATCAGACCTTGTTTCAAAGTGGATGGGTGAAAGTGAAAAGCTGGTTTCAAACCTTTTCGAAATGGCTCGAGAAAGTGCCCCTTCTATCATA
upper sequence: LOC_Os01g04814.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA12G30910.1 (Glycine max), 3'ss of exon 2
tgatgttgccaatgatcaatatcaatgtataccat-attcatttgtattgttcgtgcaatatattttattatgtttcatttaatgt-gtttgctttatgcagTATATCTTCATCAGACCTTGTTTCAAAATGGATGGGAGAGAGTGAAAAACTTGTTGCAAACCTTTTCCAAATGGCTCGAGAAAACGCTCCTTCCATTATC
|| | | || | || | | || | || || | | | | || || | | | | || | | | | | ||| || |||| | ||||||||||||||||||||||| |||||||| || |||||||| || ||| ||||||||||| ||||||||||||||| || ||||| || ||
-cttgatatctattaaaaaaggtcttttgtattgttatgaatgtaggtccataagtggacatgttcttgcaagcatttttaacttttgaattcttcat-cagTGTTTCTTCATCAGACCTTGTTTCAAAGTGGATGGGTGAAAGTGAAAAGCTGGTTTCAAACCTTTTCGAAATGGCTCGAGAAAGTGCCCCTTCTATCATA
upper sequence: LOC_Os01g04814.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv13s0106g00490.t01 (Vitis vinifera), 3'ss of exon 2
tgatgttgccaatgatcaatatcaatgtataccatattcatttgtattgttcg-tgcaatatattttattatgtttcattta--atgtgtttgctttatgcagTATATCTTCATCAGACCTTGTTTCAAAATGGATGGGAGAGAGTGAAAAACTTGTTGCAAACCTTTTCCAAATGGCTCGAGAAAACGCTCCTTCCATTATC
| | | | | ||| |||| | || | || | | | | | || | || || | | | || |||| |||| | |||||||| || || ||||||||||||||||| || |||||||| || || |||| || || ||||||||||| |||| ||||||||||| ||
---tacaaacgaaagaagggttggcttaatatcatagatacaggtttattttgatagacttgagcctacaaagtcacaaatgccaaatattgtctttccacagTGTGTCTTCATCTGATCTAGTTTCAAAATGGATGGGTGAAAGTGAAAAGCTAGTCTCAAATCTGTTTCAAATGGCTCGTGAAAGTGCTCCTTCCATCATT
upper sequence: LOC_Os01g04814.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv06s0080g00160.t01 (Vitis vinifera), 3'ss of exon 2
-----tgatgttgccaatgatcaatatcaatgtataccatattcatttgtatt-gttcgtgcaatatattttattatgtttcatttaatgtgtttgctttatgcagTATATCTTCATCAGACCTTGTTTCAAAATGGATGGGAGAGAGTGAAAAACTTGTTGCAAACCTTTTCCAAATGGCTCGAGAAAACGCTCCTTCCATTATC
|| | || || | | | | | | | || || | || | | || | ||| || | || || | ||| || |||||| | ||||| |||||||| |||||||| |||||||| || |||||||| | ||| |||| ||||| ||||||||||| || | ||||||||||| |||
aagtctgtttctgtttctggttatcgtatttttctcctccttttatgttcatgagcttaggcca-ataagttggcaagtgccaactgctgt-----tcttttgcagTGTCTCTTCTTCAGACCTGGTTTCAAAGTGGATGGGTGAAAGTGAAAAGTTAGTTTCAAATCTTTTTCAAATGGCTCGGGAGAGTGCTCCTTCCATCATC
upper sequence: LOC_Os01g04814.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S200_72V6.1 (Physcomitrella patens), 3'ss of exon 2
--------------------------------------------------------------------------------------------tgatgttgccaatgatc-aatatcaatgtataccatattcatttgtattgttcgtgcaatatattttatta-tgtttcatttaatgtgtttgctttat--gcagTATATCTTCATCAGACCTTGTTTCAAAATGGATGGGAGAGAGTGAAAAACTTGTTGCAAACCTTTTCCAAATGGCTCGAGAAAACGCTCCTTCCATTATC
| | | ||| ||| | | | || || | || | | | | | | | | || | | | | | | | |||| | ||||||| || || || ||| | || ||||| |||||||||||||| || |||||||||||||| || || |||||||| | ||| ||||| ||||||||
gtaactggagaagcatatatgcaaacaacaatgattttgttggatgcattttctttttgttttgttgcaataatcactattccagacttgggtcaaatgaagaataatctgagaagagtgggtaataaggtcttccaagct-tcaggatgttgtgaatggtggctgcgtgactgattttttaaactttctctgcagTATTTCCTCTTCTGACTTGGTGTCAAAGTGGATGGGAGAGAGCGAGAAACTTGTTGCAAATCTGTTTCAAATGGCCCATGAAGCTGCTCCATCCATTATT
upper sequence: LOC_Os01g04814.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S76_197V6.1 (Physcomitrella patens), 3'ss of exon 2
-------------------------------------------tgatgttgcc--aatgatcaatat--caatgtataccatattcatttgtattgttcgtgcaatatatttta--ttatgtttc----atttaatgtgtttgctttatgcagTATATCTTCATCAGACCTTGTTTCAAAATGGATGGGAGAGAGTGAAAAACTTGTTGCAAACCTTTTCCAAATGGCTCGAGAAAACGCTCCTTCCATTATC
| ||| | ||||| ||| | | | | | || | | | |||| || | || ||| | | | | | | | |||||||| || || |||||| | || ||||| ||||||||||||||||| || ||||||||||| || || |||||||| || ||| ||||| ||||| |||
gtaactgtcgaagcataatttggacacgatcatcttgtattaccaactttggctaaatgaagaattctccgggacgagcgagaaatgaggttgttaaacctttagtatacttggactggtggttctgggactgattattactttcctctgcagTATTTCCTCTTCAGACTTGGTGTCAAAGTGGATGGGAGAGAGTGAGAAGCTTGTTGCAAATCTGTTTCAAATGGCCCGTGAAGCTGCTCCATCCATCATCMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|300215967|gb|HO088593.1|HO088593EST: TCTTATTTGGCTAAAGCTGTTGCAACTGAGGCTGATTCTACATTTTTCAG TATATCTTCATCAGACCTTGTTTCAAAATGGATGGGAGAGAGTGAAAAACT
genomic: TCTTATTTGGCTAAAGCTGTTGCAACTGAGGCTGATTCTACATTTTTCAGgtagttatac ... ctttatgcagTATATCTTCATCAGACCTTGTTTCAAAATGGATGGGAGAGAGTGAAAAACT
EST:
gi|33381146|gb|CF196489.1|CF196489EST: TCTTATTTGGCTAAAGCTGTTGCAACTGAGGCTGATTCTACATTTTTCAG TATATCTTCATCAGACCTTGTTTCAAAATGGATGGGAGAGAGTGAAAAACT
genomic: TCTTATTTGGCTAAAGCTGTTGCAACTGAGGCTGATTCTACATTTTTCAGgtagttatac ... ctttatgcagTATATCTTCATCAGACCTTGTTTCAAAATGGATGGGAGAGAGTGAAAAACT
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
73 (upstream exon),
58 (downstream exon)
Score:
30GGAGACCATGGAGGGCTTTTCTTTTGTATGGTCCACCAGGAACAGGAAAGTCTTATTTGGCTAAAGCTGTTGCAACTGAGGCTGATTCTACATTTTTCAGgtagttatac ... ctttatgcagTATATCTTCATCAGACCTTGTTTCAAAATGGATGGGAGAGAGTGAAAAACTTGTTGCAAACCTTTTCCAAATGGCTCGAGAAAACGCTCCTTCCATTATC
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgttcgtgcaatatattttattatgtttcatttaatgtgtttgctttatgcagTATATCTTCATCAGACCTTGTTTCAAAATGGATGGGAGAGAGTGAAAAACTTGTTGCAAACCTTTTCCAAATGGCTCGAGAAAACGCTCCTTCCATTATC
atttaat putative branch site (score: 30)
tttgcttt putative PPT
aatatattttattatg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgatgttgccaatgatcaatatcaatgtataccatattcatttgtattgttcgtgcaatatattttattatgtttcatttaatgtgtttgctttatgcagTATATCTTCATCAGACCTTGTTTCAAAATGGATGGGAGAGAGTGAAAAACTTGTTGCAAACCTTTTCCAAATGGCTCGAGAAAACGCTCCTTCCATTATC
- -tgttgcc
- - - - - - - - - - - - - - - - - - - - - tgtattg
- - - - - - - - - - - - - - - - - - - - - - - - - -cgtgcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgtttg