Sequence
atgc intronic sequence ATGC exonic sequencegtaaagacaatatagagcactgtggctccactcttttctagctggttgggatactggtccctctcgactgttttcttcctatggggacgtgtctaaattgttctcctctctgcagCTATCTTTCCAAGAATGGACTCAACAGATGAGAGATATGTTGGATGCTAGGAAACGTGGTGATTTTGCATTTCGAGACAAAAATTTCAAGCAAGCCATAG
Basic information
species | Oryza sativa |
transcript | LOC_Os10g39670.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os10g39670.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G026767_T01 (Zea mays), 3'ss of exon 6
gtaaagacaatatagagcactgtggctccactcttttctagctggttgggatactggtccctctcgactgttttcttcctatggggacgtgtctaaattgttctcctctctgcagCTATCTTTCCAAGAATGGACTCAACAGATGAGAGATATGTTGGATGCTAGGAAACGTGGTGATTTTGCATTTCGAGACAAAAATTTCAAGCAAGCCATAG
||||| | || || ||||| ||| |||| |||| ||| | ||| ||||| | | || |||||| ||||||||| ||||| ||||||||||| || |||||||| |||||| ||||||| ||||||||||| || | ||| || ||||||| |||| ||| ||| || |
gtaaa-ataaaccagtgcactctggttccaatcttcatgttctg--tagga--------cctctgaa-----------------------accagcatcattctccattctgcagCTGTCTTTTCAAGAATGGACACAGCAGATGAGGGATATGCTGGATGCAAGGAAACGTGGCGACTCTGCCTTCAAAGACAAAGATTTTAAGGCAGCAATCG
upper sequence: LOC_Os10g39670.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA02G48030.1 (Glycine max), 3'ss of exon 5
gtaaagacaatatagagcactgtggctccactcttttctagctggttgggatactgg-tccctctcgactgttttcttcctatggggacgtgtctaaatt---gttctcctctctgcagCTATCTTTCCAAGAATGGACTCAACAGATGAGAGATATGTTGGATGCTAGGAAACGTGGTGATTTTGCATTTCGAGACAAAAATTTCAAGCAAGCCATAG
|| ||| | || | ||| | | ||| |||| | | | | || || | | ||| | || |||||||| |||||||||||||||||||||||| |||| || ||||| ||||| || | |||||| || ||||| | || ||| |||||| |
-------------------------------------gtaactgatgggtgcattgggtttaaatttactatttttggttggatgatatgccataaggtttgaatttggattggttcagTTGTCGTTCCAAGAGTGGACTCAACAGATGAGAGATATGCTGGAGGCAAGGAAGCGTGGAGACTATGCATTCCGTGACAAGGACTTTAAGACAGCCATTG
upper sequence: LOC_Os10g39670.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA14G00540.1 (Glycine max), 3'ss of exon 5
gtaaagacaatatagagcactgtggctccactcttttctagctggttgggatactggtccctc-tcgactgttttcttcctatggggacgtgtctaaatt---gttctcctctctgcagCTATCTTTCCAAGAATGGACTCAACAGATGAGAGATATGTTGGATGCTAGGAAACGTGGTGATTTTGCATTTCGAGACAAAAATTTCAAGCAAGCCATAG
|| ||| | || | |||| | ||| |||| | | | || || | | ||| | ||||| ||||| |||||||||||||||||||||||| |||| || ||||| || || || |||||| || ||||| | || | | |||||| |
-------------------------------------gtaactgatgggtgcattggttttaaatttactatttttaattggatgatgtgccataaggtttgaatttggattggttcagTTGTCTTTTCAAGAGTGGACTCAACAGATGAGAGATATGCTGGAAGCAAGGAAGCGCGGAGACCATGCATTCCGTGACAAGGACTTTAGGACAGCCATTG
upper sequence: LOC_Os10g39670.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT4G35230.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaaagacaatatagagcactgtggctccactcttttctagctggttggga-tactggtccctctcgactgttttcttcctatggggacgtgtctaaatt-----gttctcctct---ctgcagCTATCTTTCCAAGAATGGACTCAACAGATGAGAGATATGTTGGATGCTAGGAAACGTGGTGATTTTGCATTTCGAGACAAAAATTTCAAGCAAGCCATAG
|| ||| | | |||| | | | | ||| | | | | || |||| || ||| || | | ||| |||| |||||||||||||||||||| |||| ||||||| | ||||| ||||||| |||||| | || || || ||| ||||||| |||||| |
-------------------------------------gtaatcaaatggtagttttggtttcaattgctaaaatgctttaaaaagagtcttgactaacttttggggtttatctatggatttcagTTATCATTCCAAGAATGGACTCAACAAATGAAAGATATGCTTGATGCACGGAAACGCGGTGATCAATCTTTCCGCGAGAAAGATTTCAAAACAGCCATCG
upper sequence: LOC_Os10g39670.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv18s0001g00180.t01 (Vitis vinifera), 3'ss of exon 7
gtaaagacaatatagagcactgtggctccactcttttctagctggttgggatactggtccctctcgactgttttcttcctatggggacgtgtctaaattgttctcctctctgcagCTATCTTTCCAAGAATGGACTCAACAGATGAGAGATATGTTGGATGCTAGGAAACGTGGTGATTTTGCATTTCGAGACAAAAATTTCAAGCAAGCCATAG
| | || | || || | || | | | |||| || ||| | ||||| | | | ||||| | | ||||| ||||||||||||||||||| ||||| |||||||||||| | || || || || ||||| || || ||||| || |||||| |||| || ||||||||
------------------------gtacttgatttctacagatg-taggtttgcagatccccatc------tttaattctatgctaaattctttaaatgtatgtggataatgcagTTATCTTTCCAAGAATGGACACAACAAATGAGAGATATGCTTGAGGCAAGAAAGCGTGGGGACTTAGCATTCCGTGACAAAGATTTTAAAACAGCCATAG
upper sequence: LOC_Os10g39670.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv03s0038g03270.t01 (Vitis vinifera), 3'ss of exon 7
gtaaagacaatatagagcactgtggctccactcttttctagctggttgggatactggtccctctcgactgttttcttcctatggggacgtgtctaaattgttctcctctctg--cagCTATCTTTCCAAGAATGGACTCAACAGATGAGAGATATGTTGGATGCTAGGAAACGTGGTGATTTTGCATTTCGAGACAAAAATTTCAAGCAAGCCATAG
|| | | || | |||| | ||| |||| ||| || | ||| |||| || || || ||| | | | | | ||| | || |||||||||||||| |||||||||||||||||| | || || ||||| ||||| || |||||||| || ||||| |||| || ||||| |
---------------------gtaattgagttgttgatgaa--ggttttt-ttttggcatctctatact-cttacatccaatggtgagtggtttatcttggtgttgtattggttcagTTGTCCTTCCAAGAATGGACCCAACAGATGAGAGATATGCTAGAAGCAAGGAAGCGTGGGGACTTTGCATTCCGTGACAAGGATTTTAAAACTGCCATTGMapped 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|218489546|gb|FG966243.1|FG966243EST: ATCAGATCCTAGTTTCGACACATTACAGAGATGATGAAGGGACTAATGAG CTATCTTTCCAAGAATGGACTCAACAGATGAGAGATATGTTGGACGCTAGG
genomic: ATCAGATCCTAGTTTCAACACATTACAGAGATGATGAAGGGACTAATGAGgtaaagacaa ... ctctctgcagCTATCTTTCCAAGAATGGACTCAACAGATGAGAGATATGTTGGATGCTAGG
EST:
gi|58656973|gb|CK045653.1|CK045653EST: ATCAGATCCTAGTTTCAACACATTACAGAGATGATGAAGGGACTAATGAG CTATCTTTCCAAGAATGGACTCAACAGATGAGAGATATG
genomic: ATCAGATCCTAGTTTCAACACATTACAGAGATGATGAAGGGACTAATGAGgtaaagacaa ... ctctctgcagCTATCTTTCCAAGAATGGACTCAACAGATGAGAGATATG
EST:
gi|569871|gb|D40720.1|D40720EST: ATCAGATCCTAGTTTCAACACATTACAGAGATGATGAAGGGACTAATGAG CTATCTTTTCAAGAATGGACTCAACAGATGAGAGATATGTTGGATGCTAGG
genomic: ATCAGATCCTAGTTTCAACACATTACAGAGATGATGAAGGGACTAATGAGgtaaagacaa ... ctctctgcagCTATCTTTCCAAGAATGGACTCAACAGATGAGAGATATGTTGGATGCTAGG
EST:
gi|58595248|gb|CF993556.1|CF993556EST: ATCAGATCCTAGTTTCAACACATTACAGAGATGATGAAGGGACTAATGAG CTATCTTTCCA
genomic: ATCAGATCCTAGTTTCAACACATTACAGAGATGATGAAGGGACTAATGAGgtaaagacaa ... ctctctgcagCTATCTTTCCA
EST:
gi|29663195|gb|CB659470.1|CB659470EST: ATCAGATCCTAGTTTCAACACATTACAGAGATGATGAAGGGACTAATGAG CTATCTTTCCAAGAATGGACTCAACAGATGAGAGATATGTTGGATGCTAGG
genomic: ATCAGATCCTAGTTTCAACACATTACAGAGATGATGAAGGGACTAATGAGgtaaagacaa ... ctctctgcagCTATCTTTCCAAGAATGGACTCAACAGATGAGAGATATGTTGGATGCTAGG
EST:
gi|66918229|gb|CX105077.1|CX105077EST: GTTTCAACACATTACAGAGATGATGAAGGGACTAATGAG CTATCTTTCCAAGAATGGACTCCACAGATGAGAGATATGTTGGATGCTAGG
genomic: GTTTCAACACATTACAGAGATGATGAAGGGACTAATGAGgtaaagacaa ... ctctctgcagCTATCTTTCCAAGAATGGACTCAACAGATGAGAGATATGTTGGATGCTAGG
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:
42 (upstream exon),
73 (downstream exon)
Score:
7ACTTTCTCCCATGGGAGAGGCCTGTTCCAGGATGGACCTTACTGCCATCCATCAGATCCTAGTTTCAACACATTACAGAGATGATGAAGGGACTAATGAGgtaaagacaa ... ctctctgcagCTATCTTTCCAAGAATGGACTCAACAGATGAGAGATATGTTGGATGCTAGGAAACGTGGTGATTTTGCATTTCGAGACAAAAATTTCAAGCAAGCCATAG
<
<
<
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctctcgactgttttcttcctatggggacgtgtctaaattgttctcctctctgcagCTATCTTTCCAAGAATGGACTCAACAGATGAGAGATATGTTGGATGCTAGGAAACGTGGTGATTTTGCATTTCGAGACAAAAATTTCAAGCAAGCCATAG
gtctaaa putative branch site (score: 7)
ttgttctcctctctgc CT-rich tract
taaattgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaagacaatatagagcactgtggctccactcttttctagctggttgggatactggtccctctcgactgttttcttcctatggggacgtgtctaaattgttctcctctctgcagCTATCTTTCCAAGAATGGACTCAACAGATGAGAGATATGTTGGATGCTAGGAAACGTGGTGATTTTGCATTTCGAGACAAAAATTTCAAGCAAGCCATAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG