Sequence
atgc intronic sequence ATGC exonic sequencegttagtcttctgacaacacttgtgatgttcccaattgctgtttaccatggaattttattgttaacaatacaaacatttgattcatctgcagGTGATTTCTTCCGCTCATTTTTGACAGAGGACAAGGCACCTGGTGGCCTTTCCTATGTGGAGTTCCTTGTGCATGTGCACAGGCAAATCCAGAGCAAGAT
Basic information
species | Oryza sativa |
transcript | LOC_Os11g29200.1 |
intron # | 23 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g29200.1 (Oryza sativa), 3'ss of exon 23
lower sequence: GRMZM2G142697_T02 (Zea mays), 3'ss of exon 7
--------gttagtcttctgacaacacttgtgatgttcccaattgctgtttaccatggaattttattgttaacaataca--aacatttgattcatctgcagGTGATTTCTTCCGCTCATTTTTGACAGAGGACAAGGCACCTGGTGGCCTTTCCTATGTGGAGTTCCTTGTGCATGTGCACAGGCAAATCCAGAGCAAGAT
| | | || | ||| || | | ||| || | | |||| ||| || | || | | ||||| ||| ||||||||||||| ||||| |||||||| ||||||||||| ||||| | | | ||||| || ||||||||||||||||| |||||||||||||| ||||||||
ttccaatggaaaataaactaattttctttgcgaagatgaaaatctcttgtgaaaatggtgtttccaaactagccctaaatggatatttggttc-cctgcagGTGATTTTTTCCGGTCATTTTTAGTGGAGGACAAGGCGCCTGGCGTCTTCTCCTACGTCGAGTTCCTTGTGCATGTCCACAGGCAAATCCAAAGCAAGAT
upper sequence: LOC_Os11g29200.1 (Oryza sativa), 3'ss of exon 23
lower sequence: GRMZM2G019236_T05 (Zea mays), 3'ss of exon 22
gttagtcttctga-caacacttgtgatg------------ttcccaattgctgtttaccatgga-------------attttat----tgttaacaata---caaacatttgattcatctgcagGTGATTTCTTCCGCTCATTTTTGACAGAGGACAAGGCACCTGGTGGCCTTTCCTATGTGGAGTTCCTTGTGCATGTGCACAGGCAAATCCAGAGCAAGAT
||||||||||||| |||| | || | | | |||| | || ||| | || |||| || | || ||||| ||| ||||||| ||||| ||||| |||||| | | |||||||||||||||||| | | | ||||| | |||||| || |||||||| |||||||| ||||| ||||||||
gttagtcttctgagcaactcatgagccgaccggttattaacccataattattagttgtagcggagaaagaaaaagaaaccctacaaggtgtttacgcctgaccgaatatttggttc-cctgcagGAGATTTTTTCCGGTCATTTCTAATAGAGGACAAGGCACCTGGCGTCTTCTCCTACGAGGAGTTTCTCGTGCATGTCCACAGGCAGATCCAAAGCAAGAT
upper sequence: LOC_Os11g29200.1 (Oryza sativa), 3'ss of exon 23
lower sequence: EFJ37281 (Selaginella moellendorffii), 3'ss of exon 4
------gttagtcttctgacaacacttgtgatgttcccaattgctgtttaccatggaattttattgttaacaatac----aaacatttgattcatctgcagGTGATTTCTTCCGCTCATTTTTGACAGAGGACAAGGCACCTGGTGGCCTTTCCTATGTGGAGTTCCTTGTGCATGTGCACAGGCAAATCCAGAGCAAGAT
||| || | | | ||| | | || | |||| || || || |||| | || | ||| | |||| ||| || | || || | ||| | ||||| |||||||||||||||| | ||||||||||||||||||
ttctaggttgcatttgctgaagcggg-gagatcctttaggtgatcaaacacactcattttttctttttcgaggcactcttgctcattcggttttgttacagAGATGATGTTCCACTC---CTTAAGAGCGGGCTGGGCTC------GCCTT----ATGTGGAGTTCCTTGTCTACGTGCACAGGCAAATCCAG--------
upper sequence: LOC_Os11g29200.1 (Oryza sativa), 3'ss of exon 23
lower sequence: EFJ22499 (Selaginella moellendorffii), 3'ss of exon 10
gttagtcttctgacaacacttgtgat-gttcccaattgctgtttaccatggaattttattgttaacaatacaaacatttgattcatctgcagGTGATTTCTTCCGCTCATTTTTGACAGAGGACAAGGCACCTGGTGGCCTT-TCCTATGTGGAGTTCCTTGTGCATGTGCACAGGCAAATCCAGAGCAAGAT
||||| | | | | ||| || || | | || |||| | || | ||| | |||| ||| || ||| ||||||||| | | ||| || || ||||||||||||||||| | ||||||||||||||||||
---------------------gtgatcaaacactctcatttttttccttgtcgaagcactcttgct--------cattcggttttgttacagAGATGATGTTCCACTCCTTCATGATCGAGGACAAGA-GCGGGCTGGGCTCGTCTTATGTGGAGTTCCTTGTCTACGTGCACAGGCAAATCCAG--------
upper sequence: LOC_Os11g29200.1 (Oryza sativa), 3'ss of exon 23
lower sequence: EFJ27667 (Selaginella moellendorffii), 3'ss of exon 23
gttagtcttctgacaacacttgtgatgttcccaattgctgtttaccatggaattttattgttaacaatacaaacatttgattcatctgcagGTGATTTCTTCCGCTCATTTTTGACAGAGGACAAGGCACCTGGTGGCCTT-TCCTATGTGGAGTTCCTTGTGCATGTGCACAGGCAAATCCAGAGCAAGAT
| | || || || | | | | | ||| | |||| | || | ||| | |||| ||| || ||| ||||||||| | | ||| || || ||||||||||||||||| | |||||||||||||||||| || ||
---------------gtgatca-aacactctcattttttttctttttcgaggcactcttgct-----------cattcggttttgttacagAGATGATGTTCCACTCCTTCATGATCGAGGACAAGA-GCGGGCTGGGCTCGTCTTATGTGGAGTTCCTTGTCTACGTGCACAGGCAAATCCAGGTAAAAAT
upper sequence: LOC_Os11g29200.1 (Oryza sativa), 3'ss of exon 23
lower sequence: EFJ37282 (Selaginella moellendorffii), 3'ss of exon 23
gttagtcttctgacaacacttgtgatgttcccaattgctgtttaccatggaattttattgttaacaatacaaacatttgattcatctgcagGTGATTTCTTCCGCTCATTTTTGACAGAGGACAAGGCACCTGGTGGCCTT-TCCTATGTGGAGTTCCTTGTGCATGTGCACAGGCAAATCCAGAGCAAGAT
|| ||| || | | |||| | | | | |||| | || | ||| | |||| ||| || ||| || |||||| | | ||| || || ||||||||||||||||| | |||||||||||||||||| || ||
--------------------------gtgatcaaacactctcatttttttctttttcgaggcactcttgct--cattcggttttgttacagAGATGATGTTCCACTCCTTCATGATCGAAGACAAGA-GCGGGCTGGGCTCGTCTTATGTGGAGTTCCTTGTCTACGTGCACAGGCAAATCCAGGTAAAAATMapped 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|88688653|gb|CI732229.1|CI732229EST: GTTGCGTCTATGCAGAAGGGGTGAACCATCTG GTGATTTCTTCCGCTCATTTTTGACAGAGGACAAGGCACCTGGTGGCCTTT
genomic: GTTGCGTCTATGCAGAAGGGGTGAACCATCTGgttagtcttc ... tcatctgcagGTGATTTCTTCCGCTCATTTTTGACAGAGGACAAGGCACCTGGTGGCCTTT
EST:
gi|88846448|gb|CI373216.1|CI373216EST: GTTGCCTCTATGCAGAAGGGGTGAACCATCTG GTGATTTCTTCCGCTCAGTTTGGACAGAGGACAAGGCACCTGGTGGCCTTT
genomic: GTTGCGTCTATGCAGAAGGGGTGAACCATCTGgttagtcttc ... tcatctgcagGTGATTTCTTCCGCTCATTTTTGACAGAGGACAAGGCACCTGGTGGCCTTT
EST:
gi|33797787|gb|CF324753.1|CF324753EST: GTTGCGTCTATGCAGAAGGGGTGAACCATCTG GTGATTTCTTCCGCTCATTTTTGACAGAGGACAAGGCACCTGGTGGCCTTT
genomic: GTTGCGTCTATGCAGAAGGGGTGAACCATCTGgttagtcttc ... tcatctgcagGTGATTTCTTCCGCTCATTTTTGACAGAGGACAAGGCACCTGGTGGCCTTT
EST:
gi|66913440|gb|CX100288.1|CX100288EST: GTTGCGTCTATGCAGAACGGGTGAACCATCTG GTGATTTCTTCCGCTCATTTTTGACAGAGGACA
genomic: GTTGCGTCTATGCAGAAGGGGTGAACCATCTGgttagtcttc ... tcatctgcagGTGATTTCTTCCGCTCATTTTTGACAGAGGACA
EST:
gi|33680475|gb|CF308714.1|CF308714EST: GTTGCGTCTATGCAGAAGGGGTGAACCATCTG GTGATTTCTTCCGCTCATTTTTGACAGAGGACAAGGCACNCTGGTGGCCTT
genomic: GTTGCGTCTATGCAGAAGGGGTGAACCATCTGgttagtcttc ... tcatctgcagGTGATTTCTTCCGCTCATTTTTGACAGAGGACAAGGCAC-CTGGTGGCCTT
EST:
gi|88691349|gb|CI733932.1|CI733932EST: GTTGCGTCTATGCAGAAGGGGTGAACCATCTG GTGATTTCTTCCGCTCATTTCTGACAGAGGACAAGGCACCTGGTGGCCTTT
genomic: GTTGCGTCTATGCAGAAGGGGTGAACCATCTGgttagtcttc ... tcatctgcagGTGATTTCTTCCGCTCATTTTTGACAGAGGACAAGGCACCTGGTGGCCTTT
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:
32 (upstream exon),
63 (downstream exon)
Score:
25GTTGCGTCTATGCAGAAGGGGTGAACCATCTGgttagtcttc ... tcatctgcagGTGATTTCTTCCGCTCATTTTTGACAGAGGACAAGGCACCTGGTGGCCTTTCCTATGTGGAGTTCCTTGTGCATGTGCACAGGCAAATCCAGAGCAAGAT
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctgtttaccatggaattttattgttaacaatacaaacatttgattcatctgcagGTGATTTCTTCCGCTCATTTTTGACAGAGGACAAGGCACCTGGTGGCCTTTCCTATGTGGAGTTCCTTGTGCATGTGCACAGGCAAATCCAGAGCAAGAT
ttcatct CT-rich tract
aattttattgttaaca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtcttctgacaacacttgtgatgttcccaattgctgtttaccatggaattttattgttaacaatacaaacatttgattcatctgcagGTGATTTCTTCCGCTCATTTTTGACAGAGGACAAGGCACCTGGTGGCCTTTCCTATGTGGAGTTCCTTGTGCATGTGCACAGGCAAATCCAGAGCAAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA