Sequence
atgc intronic sequence ATGC exonic sequencegttagttttttgcttcataaaatgttgcttgacaaatgaaaattcaaacatcaattaatgttcttctgtcgtggtgtttcagCTGTCAATAAGGATGAGCTATTGCAGATGGTCAGATTTGGTGCTGAAATGGTATTCAGCTCCAAGGATAGCACAATAACAGATGAAGATATTGACCGCAT
Basic information
species | Oryza sativa |
transcript | LOC_Os05g05780.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 13
lower sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 13
-------------------gttagttttttgcttcataaaatgttgcttgacaaatgaaaattcaaacatcaattaatgttcttctgtcgtggtgtttcagCTGTCAATAAGGATGAGCTATTGCAGATGGTCAGATTTGGTGCTGAAATGGTATTCAGCTCCAAGGATAGCACAATAACAGATGAAGATATTGACCGCAT
|| | | |||| |||| | | || || | || | || | || || ||||| | | || |||||||||||||||||| || |||| ||||| | ||||||||||||||||| ||||| || ||||| ||||||||||| ||||| || |||||||| ||
gtatggttatgatatttgcctttgctatttgtttcaagcatttttctttactagttggatatggattattctgacaacattcttttttg-------ttaagCTGTCAATAAGGATGACCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGGTTTTCAGTTCTAAGGACAGCACAATAACTGATGAGGACATTGACCGTAT
upper sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 10
gttagttttttgcttcataaaatgttgcttgacaaatgaaaattcaaaca--tcaattaatgttcttctg-------tcgtggtgtttcagCTGTCAATAAGGATGAGCTATTGCAGATGGTCAGATTTGGTGCTGAAATGGTATTCAGCTCCAAGGATAGCACAATAACAGATGAAGATATTGACCGCAT
|| | |||| | | | | ||| | | | || | | | || || ||||| || | || |||||||||||||||||| || |||| ||||| | ||||||||||||||||| ||||| || ||||| ||||||||||| ||||| || |||||||| ||
gtatggttttgatatttgccatttctatttgttttaagcattttttactagtttgatctggattgttctgacaacattctcatttattaagCTGTCAATAAGGATGATCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGGTTTTCAGTTCTAAGGACAGCACAATAACTGATGAGGACATTGACCGTAT
upper sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 13
----------------gttagttttttgcttcataaaatgttgcttgacaaatgaaaattcaaacatcaattaatgttcttctgtcgtggtgtttcagCTGTCAATAAGGATGAGCTATTGCAGATGGTCAGATTTGGTGCTGAAATGGTATTCAGCTCCAAGGATAGCACAATAACAGATGAAGATATTGACCGCAT
||| || | || || ||||||| || ||| | | ||||| | | ||| | || | ||||||| ||||| |||||| | | || ||||| |||||||||||||||||||| || || |||||||| || ||||| |||||||| ||||||||| | ||
gtaagggtttctggattttatcttcgtttttattattttgttgctagatttatggattatataacat-ggtacacaatctatttgtgta----tgcagCTGTTAATAAAGATGAGTTGCTTCAAATGGTTAGATTTGGTGCTGAAATGGTTTTTAGTTCCAAGGACAGTACAATTACAGATGAGGATATTGACAGAAT
upper sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 13
---------------gttagttttttgcttcataaaatgttgcttgacaaatgaaaattcaaacatcaattaatgttcttctgtcgtggtgtttcagCTGTCAATAAGGATGAGCTATTGCAGATGGTCAGATTTGGTGCTGAAATGGTATTCAGCTCCAAGGATAGCACAATAACAGATGAAGATATTGACCGCAT
||| | |||| || || || ||| | | | ||| | | | | || | ||| | || | ||||||| ||||| |||||| | | || ||||| |||||||||||||||||||| || || |||||||| || ||||| |||||||| ||||||||| | ||
gtaagggttttctgggttttatctttgtttt-tattattttgttgcaagattgatggattatataacatggtacaatctatttgtgta----tgcagCTGTAAATAAAGATGAGTTGCTTCAAATGGTTAGATTTGGTGCTGAAATGGTTTTTAGTTCCAAGGACAGTACAATTACAGATGAGGATATTGACAGAAT
upper sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 13
gttagttttttgcttcataaaatgt--tgcttgacaaatgaaaatt-caaacatcaattaatgttcttctgtcgtggtgttt---cagCTGTCAATAAGGATGAGCTATTGCAGATGGTCAGATTTGGTGCTGAAATGGTATTCAGCTCCAAGGATAGCACAATAACAGATGAAGATATTGACCGCAT
||| || | |||| | | || || ||||| || || |||| | ||| | | | | | |||| || ||||| ||||| | | || ||||| |||||||| ||||||||||| ||||| ||||||||||| ||||| ||||||||||||||||| | ||
-gtaggaattcaatgaataacttttcttgtttctttgctgaaagttgtgtggattgtctaatatggttccattggcttttatgtgcagCGGTAAATAAAGATGAATTGCTTCAAATGGTTAGATTTGGGGCTGAAATGGTTTTCAGTTCCAAGGATAGTACAATTACAGATGAAGATATTGATAGAAT
upper sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 13
--gttagttttttgcttcataaaatgttgcttgacaaatgaaaatt-caaacatcaattaatgttcttctgtcgtggtgttt---cagCTGTCAATAAGGATGAGCTATTGCAGATGGTCAGATTTGGTGCTGAAATGGTATTCAGCTCCAAGGATAGCACAATAACAGATGAAGATATTGACCGCAT
| || || | || | ||| || ||||| || || |||||| ||| | | | | | |||| || ||||| |||||| | | || ||||| |||||||| ||||||||||| ||||| ||||||||||| ||||| |||||||| |||||||| | ||
gtatggattcaatgaataatttt-tcttgtttctttgctgaaagttgtgtggattgtctaatgtggttccattgatttttatgtgcagCGGTAAATAAAGATGAGTTGCTTCAAATGGTTAGATTTGGGGCTGAAATGGTTTTCAGTTCCAAGGATAGTACAATTACAGATGAGGATATTGATAGAAT
upper sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 13
lower sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 13
gttagttttttgcttcataaaatg-ttgcttgacaaatgaaaattcaaacatcaattaatgttcttctgtcgtggtgtttcagCTGTCAATAAGGATGAGCTATTGCAGATGGTCAGATTTGGTGCTGAAATGGTATTCAGCTCCAAGGATAGCACAATAACAGATGAAGATATTGACCGCAT
| ||| | ||| | || |||||| | || |||| | | ||| | | || | | |||||||||||||||||||| | | || ||||| |||| ||||||||| ||||| ||||| || || ||||||||||| ||||| || |||||||| | ||
-----gtaagtgcgttatacagtgattgctttatgcattgg--ttcatctctgacagaattggtatttatcttaactatgcagCTGTCAATAAGGATGAGTTGCTTCAAATGGTAAGATATGGTGCTGAGATGGTGTTCAGTTCTAAAGATAGCACAATCACAGACGAGGATATTGATAGAAT
upper sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 13
lower sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 13
gttagttttttgcttcataaaatgttgcttgacaaatgaaaatt---caaacatcaat-taatgttcttctgtcgtggtgtttcagCTGTCAATAAGGATGAGCTATTGCAGATGGTCAGATTTGGTGCTGAAATGGTATTCAGCTCCAAGGATAGCACAATAACAGATGAAGATATTGACCGCAT
|| | ||| | | | | || | || || | || | |||| || || || | | | || | | || ||||||| |||||||||||| | | || ||||| |||| ||||||||||||||| || || || || ||||||||||| || ||||| ||||||||| | ||
-gtaagtgcttgtgtactgag--gctgttagatgtattggattttctcttacatatatatactgatttcttttctttgctttccagCTGTTAATAAGGATGAGTTGCTTCAAATGGTGAGATATGGTGCTGAAATGGTGTTTAGTTCTAAAGATAGCACAATTACGGATGAGGATATTGACAGAAT
upper sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 13
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 13
---------------gttagttttttgcttcataaaatgttgc-ttgacaaatgaaaattcaaacatcaat-taatgttcttctgtcgtggtgtttcagCTGTCAATAAGGATGAGCTATTGCAGATGGTCAGATTTGGTGCTGAAATGGTATTCAGCTCCAAGGATAGCACAATAACAGATGAAGATATTGACCGCAT
||| |||||| | ||| | | || || | || || || | |||| || | | | | || ||||||| || || ||||||||| |||| |||||||| ||||||||||||||||| ||||||||||||||||||||||| || |||||||| || ||| | ||
gtgagccatttctgcattacaagcttgctttgcactatgacatgctaattcatagaactagaaccactaacattttgttgtttttgtgggcttttgcagCTGTGAACAAAGATGAGCTACTGCAAATGGTCAGGTTTGGTGCTGAAATGGTTTTCAGCTCCAAGGATAGCACAATTACGGATGAAGACATAGACAGGAT
upper sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 13
lower sequence: EFJ31365 (Selaginella moellendorffii), 3'ss of exon 13
gttagttttttgcttcataaaatgttgcttgacaaatgaaaattcaaacatcaattaatgttcttctgtcgtggtgtttcagCTGTCAATAAGGATGAGCTATTGCAGATGGTCAGATTTGGTGCTGAAATGGTATTCAGCTCCAAGGATAGCACAATAACAGATGAAGATATTGACCGCAT
||| | ||| || | | | ||| || |||| ||| || | || |||||||||| || |||||||| ||||||||||| |||||||| || || |||||||| ||| |||| || ||||| || || || ||||||||||| |||||
------------gttcctcaaactctgttatagtgtttgaaactctgtaatca----------ttccgtttcgctg---cagCTGTCAACAAAGATGAGCTCTTGCAGATGGTAAGATTTGGCGCGGAGATGGTATTTAGCGCCAATGACAGCACTATCACGGAGGAAGATATTGATCGCAT
upper sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 13
lower sequence: EFJ06565 (Selaginella moellendorffii), 3'ss of exon 13
gttagttttttgcttcataaaatgttgcttgacaaatgaaaattcaaacatcaattaatgttcttctgtcgtggtgtttcagCTGTCAATAAGGATGAGCTATTGCAGATGGTCAGATTTGGTGCTGAAATGGTATTCAGCTCCAAGGATAGCACAATAACAGATGAAGATATTGACCGCAT
| | |||| || |||| || | | ||| ||| | | |||||||||| || |||||||| ||||||||||| |||||||| || || |||||||| ||| |||| || ||||| || || || ||||||||||| |||||
--------------------------gttcctcaaactctgtttgaaac-tctgtaatcattc------cgtttcgctgcagCTGTCAACAAAGATGAGCTCTTGCAGATGGTAAGATTTGGCGCGGAGATGGTATTTAGCGCCAATGACAGCACTATCACGGAGGAAGATATTGATCGCATMapped 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|58692379|gb|CK081066.1|CK081066EST: TGCCCTGGATGCTTTGGTCATACAACAGGGTCGATTGGCAGAGCAGAAAG CTGTCAATAAGGATGAGCTATTGCAGATGGTCAGATTTGGTGCTGAAATGG
genomic: TGCCCTGGATGCTTTGGTCATACAACAGGGTCGATTGGCAGAGCAGAAAGgttagttttt ... ggtgtttcagCTGTCAATAAGGATGAGCTATTGCAGATGGTCAGATTTGGTGCTGAAATGG
EST:
gi|58657846|gb|CK046526.1|CK046526EST: TGCCCTGGATGCTTTGGTCATACAACAGGGTCGATTGGCAGAGCAGAAAG CTGTCAATAAGGATGAGCTATTGCAGATGGTCAGATTTGGTGCTGAAATGG
genomic: TGCCCTGGATGCTTTGGTCATACAACAGGGTCGATTGGCAGAGCAGAAAGgttagttttt ... ggtgtttcagCTGTCAATAAGGATGAGCTATTGCAGATGGTCAGATTTGGTGCTGAAATGG
EST:
gi|58691699|gb|CK080386.1|CK080386EST: TGCCCTGGATGCTTTGGTCATACAACAGGGTCGATTGGCAGAGCAGAAAG CTGTCAATAAGGATGAGCTATTGCAGATGGTCAGATTTGGTGCTGAAATGG
genomic: TGCCCTGGATGCTTTGGTCATACAACAGGGTCGATTGGCAGAGCAGAAAGgttagttttt ... ggtgtttcagCTGTCAATAAGGATGAGCTATTGCAGATGGTCAGATTTGGTGCTGAAATGG
EST:
gi|58694226|gb|CK082913.1|CK082913EST: TGCCCTGGATGCTTTGGTCATACAACAGGGTCGATTGGCAGAGCAGAAAG CTGTCAATAAGGATGAGCTATTGCAGATGGTCAGATTTGGTGCTGAAATGG
genomic: TGCCCTGGATGCTTTGGTCATACAACAGGGTCGATTGGCAGAGCAGAAAGgttagttttt ... ggtgtttcagCTGTCAATAAGGATGAGCTATTGCAGATGGTCAGATTTGGTGCTGAAATGG
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),
72 (downstream exon)
Score:
31TATACAATTGAGGAAAAGGTGATTGAGAGAGCTTATAAGAAGCTTGCCCTGGATGCTTTGGTCATACAACAGGGTCGATTGGCAGAGCAGAAAGgttagttttt ... ggtgtttcagCTGTCAATAAGGATGAGCTATTGCAGATGGTCAGATTTGGTGCTGAAATGGTATTCAGCTCCAAGGATAGCACAATAACAGATGAAGATATTGACCGCAT
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttgacaaatgaaaattcaaacatcaattaatgttcttctgtcgtggtgtttcagCTGTCAATAAGGATGAGCTATTGCAGATGGTCAGATTTGGTGCTGAAATGGTATTCAGCTCCAAGGATAGCACAATAACAGATGAAGATATTGACCGCAT
aattaat putative branch site (score: 31)
aaaattcaaacatcaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagttttttgcttcataaaatgttgcttgacaaatgaaaattcaaacatcaattaatgttcttctgtcgtggtgtttcagCTGTCAATAAGGATGAGCTATTGCAGATGGTCAGATTTGGTGCTGAAATGGTATTCAGCTCCAAGGATAGCACAATAACAGATGAAGATATTGACCGCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA