Sequence
atgc intronic sequence ATGC exonic sequence...ggtcagtaggtgttagaattatattatctatgctcaataatagtcgtgcaattatttaatgttggtcagtgcatatggctaatgctgttttaatcaacagGTATTGTTCTGGACTCGGGTGATGGTGTGAGCCATACTGTTCCCATCTATGAAGGATATGCACTTCCTCATGCAATCCTTCGTCTGGATCTTGCTGGCCG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g73310.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g73310.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA15G05570.1 (Glycine max), 3'ss of exon 3
ggtcagtaggtgttagaattatattatctatgc---tcaataatagtcgtg-caattatttaatgttggtcagtgcatatggctaatgctgttttaatcaacagGTATTGTTCTGGACTCGGGTGATGGTGTGAGCCATACTGTTCCCATCTATGAAGGATATGCACTTCCTCATGCAATCCTTCGTCTGGATCTTGCTGGCCG
|| | || ||| | || || |||| || | | || | || | | ||| | | | || | | | || || || | | | |||||||||||| || || || ||||||||||||||||| || || ||||| |||||||| ||||| |||||||||||||| ||||| |||| |||||||||||
attccacacgtacaagagtgggat-atacatgcatttctacattaattatgaccagcattatttccttattggtttgtcttgtta-tgttggtatta--aacagGTATTGTGCTTGATTCTGGTGATGGTGTGAGCCACACGGTGCCCATATATGAAGGGTATGCTCTTCCTCATGCAATTCTTCGGTTGGACCTTGCTGGCCG
upper sequence: LOC_Os01g73310.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA08G19420.1 (Glycine max), 3'ss of exon 3
ggtcagtaggtgttagaattatat-tatctatgctcaataatagtcgtgcaattatt-taatgttggtcagtgcatatggctaatgctgttttaatcaacagGTATTGTTCTGGACTCGGGTGATGGTGTGAGCCATACTGTTCCCATCTATGAAGGATATGCACTTCCTCATGCAATCCTTCGTCTGGATCTTGCTGGCCG
|| || | |||| | | | | | || |||| | | | | | | || | | | | | | | | | | | |||||||||||| || || || ||||||||||||||||| || |||||||| |||||||| ||||| |||||||||||||| ||||| |||| |||||||||||
-acatatacatgagtgggatatacatgtatttccacattaatt-cctcacgaccagtattatttccttattttcttgtctttgttatgttggcattaaacagGTATTGTGCTTGATTCTGGTGATGGTGTGAGCCACACAGTTCCCATATATGAAGGGTATGCTCTTCCTCATGCAATTCTTCGGTTGGACCTTGCTGGCCG
upper sequence: LOC_Os01g73310.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA08G15480.1 (Glycine max), 3'ss of exon 3
ggtcagtaggtgttagaattatattatctatgctcaataatagtcgtgcaattatttaatgttggtcagtgcatatggctaatgctgttttaatcaacagGTATTGTTCTGGACTCGGGTGATGGTGTGAGCCATACTGTTCCCATCTATGAAGGATATGCACTTCCTCATGCAATCCTTCGTCTGGATCTTGCTGGCCG
||| | || | |||| | | | | || | | ||| | ||| || | | | ||| | |||||| |||||||||||| ||||||| |||||||||||||| || ||||| || |||||||| || |||||||| || ||||| ||||||||| ||||||| ||||| ||
-----------gtttgtatatcaccatctgtcttgattcattcttttataatcac-----attgttctttccctg-aatcaattcc-ttttaa--aacagGTATTGTATTGGACTCTGGTGATGGTGTGAGTCACACTGTACCAATCTATGAGGGGTATGCACTCCCCCATGCCATCCTTCGTTTGGATCTCGCTGGTCG
upper sequence: LOC_Os01g73310.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA05G32220.1 (Glycine max), 3'ss of exon 2
ggtcagtaggtgttagaattatattatctatgctcaataatagtcgtgcaattatttaatgttggtcagtgcatatggctaatgctgttttaatcaacagGTATTGTTCTGGACTCGGGTGATGGTGTGAGCCATACTGTTCCCATCTATGAAGGATATGCACTTCCTCATGCAATCCTTCGTCTGGATCTTGCTGGCCG
||| | || || |||| | | | | || | | ||| | | || | || || || ||| | ||| || |||||||||||| ||||||| |||||||||||||| || ||||| || |||||||| || |||||||| || ||||| ||||||||| ||||||| || || ||
-----------gtttgtatattaccatctgtcttgattcattcttttataatcacatcat-tctttccctgaat-----caattcc-tttcaa--aacagGTATTGTGTTGGACTCTGGTGATGGTGTGAGTCACACTGTACCAATCTATGAGGGGTATGCACTCCCCCATGCCATCCTTCGTTTGGATCTCGCAGGTCG
upper sequence: LOC_Os01g73310.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA04G39380.2 (Glycine max), 3'ss of exon 3
ggtcagtaggtgttagaattatatt-atctatgctcaataatagtcgtgcaattatttaatgttggtcagtgcatatggctaatgctgttttaatcaacagGTATTGTTCTGGACTCGGGTGATGGTGTGAGCCATACTGTTCCCATCTATGAAGGATATGCACTTCCTCATGCAATCCTTCGTCTGGATCTTGCTGGCCG
|| || | || ||| |||| | | | ||||| || || | ||| || | | | | ||| || | | || |||||||||||| ||||||| || |||||||| || || ||||| || |||||||| || |||||||| |||||||| || |||||| ||||||||||||||||
---------gt-ttgtatttgtatccatctgtttcaattcatagttttgtcatcac-----attgttctttccctgaatcaaatactttctgaa---acagGTATTGTTTTGGACTCTGGCGATGGTGTTAGTCACACTGTGCCAATCTATGAGGGCTATGCACTCCCTCATGCCATTCTTCGTTTGGATCTTGCTGGCCG
upper sequence: LOC_Os01g73310.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA06G15520.2 (Glycine max), 3'ss of exon 3
ggtcagtaggtgttagaattatattatctatgctcaataatagtcgtgcaattat-ttaatgttggtcagtgcatatggctaatgctgttttaatcaacagGTATTGTTCTGGACTCGGGTGATGGTGTGAGCCATACTGTTCCCATCTATGAAGGATATGCACTTCCTCATGCAATCCTTCGTCTGGATCTTGCTGGCCG
||| | | | |||| || || |||| || | || | || | ||| || | | | | ||| || ||| ||||| ||||||||| ||||||| |||||||||||||| || ||||| || |||||||| || |||||||| |||||||| || || ||| ||||||||||||||||
-----------gtttgtact-tatt-tccatctgtcttaat--tcactcctttgtcttcacattgttctatccttgaatcaaat-ctttttgaatca---gGTATTGTTTTGGACTCTGGTGATGGTGTGAGTCACACTGTGCCAATCTATGAGGGCTATGCACTCCCTCATGCCATTCTCCGTTTGGATCTTGCTGGCCG
upper sequence: LOC_Os01g73310.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT5G09810.1 (Arabidopsis thaliana), 3'ss of exon 3
ggtcagtaggtgttagaattatattatctatgctcaataat-agtcgtgcaattatttaatgttggtcagtgcatatggctaatgctgttttaatcaacagGTATTGTTCTGGACTCGGGTGATGGTGTGAGCCATACTGTTCCCATCTATGAAGGATATGCACTTCCTCATGCAATCCTTCGTCTGGATCTTGCTGGCCG
||||| | | | | | ||| | ||| | || | | | | || | | || | | |||| |||||||||||| || || || |||||||||||| || ||||| || ||||| || || ||||| ||||||||||| ||||||||||| |||||||| || ||
-----------gttagttcttaactctaaacatccaagtctgagttatattatcttct--tacttgtatttacttaaagtcgttctctttttg--taacagGTATTGTGCTCGATTCTGGTGATGGTGTGTCTCACACTGTGCCAATCTACGAGGGGTATGCTCTTCCTCATGCTATCCTTCGTCTTGATCTTGCGGGTCG
upper sequence: LOC_Os01g73310.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv04s0044g00580.t01 (Vitis vinifera), 3'ss of exon 4
ggtcagtaggtgttagaattatattatctatgctcaataatagtcgtgcaattatttaatgttggtcagtgca---tatggctaatgctgttttaatcaacagGTATTGTTCTGGACTCGGGTGATGGTGTGAGCCATACTGTTCCCATCTATGAAGGATATGCACTTCCTCATGCAATCCTTCGTCTGGATCTTGCTGGCCG
||| | |||| | | | | || ||| || | || ||| ||||| | |||| | | | | || | | | ||||||||| ||||| || |||||||||||||| || ||||| || || |||||||| ||||||||||| ||||| ||||||||||| || |||||||| ||
-----------gttcgtattaaaatctttttggattggaattttcattt--ttcttttctgttg-ttagtgtagcctgagttctaacttgctcctttgactagGTATTGTGCTGGATTCTGGTGATGGTGTGAGTCACACTGTGCCAATTTATGAAGGTTATGCACTTCCCCATGCTATCCTTCGTCTTGACCTTGCTGGACG
upper sequence: LOC_Os01g73310.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv12s0178g00200.t01 (Vitis vinifera), 3'ss of exon 2
ggtcagtaggtgttagaattatattatctatgctcaataatagtcg--tgcaattatttaatgttggtcagtgc-atatg-gctaatgctgtttta---atcaacagGTATTGTTCTGGACTCGGGTGATGGTGTGAGCCATACTGTTCCCATCTATGAAGGATATGCACTTCCTCATGCAATCCTTCGTCTGGATCTTGCTGGCCG
| | | | | | | || | | ||| | || | ||| | | || || || || |||| || | | | ||| | || ||||||||| |||| || ||||||||||| |||||||| || || ||||||||||||||||| ||||| |||||||||||||| | || |||||||| ||
-------aaatttcaagaattttttcctcagtattggtaactgccgactatgattttcttatcctgttctttgttatatttactgaagttttttggtgtgtgaaaagGTATTGTCTTGGATTCTGGTGATGGTGTCAGCCATACAGTGCCAATCTATGAAGGATATGCTCTTCCACATGCAATCCTTCGATTAGACCTTGCTGGTCG
upper sequence: LOC_Os01g73310.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ35077 (Selaginella moellendorffii), 3'ss of exon 2
-----------------------------------------ggtcagtaggtgttagaattat--attatctatgctcaata---------atagtcgtgcaattatttaatgttggtcagtgcatatggc-taatgctgttttaatcaacagGTATTGTTCTGGACTCGGGTGATGGTGTGAGCCATACTGTTCCCATCTATGAAGGATATGCACTTCCTCATGCAATCCTTCGTCTGGATCTTGCTGGCCG
||| | ||||| || | || | | | | | | | || | | | ||| | || || | | | || || ||| | | ||||||||||||| ||||||||||| ||||| | || |||||||| ||||| ||||| || |||| || ||||||||||| | ||||| ||||| || ||
gtatggagttttttttttcctttgcttgttctagacaagatggttgatgcgtgtttcttttcttcgttgcttgcgatagacatgatgcttcaagttggttctacttttttttcttctctctaacacgttgtatgatcgtggtttg-tgatcagGTATTGTTCTCGACTCGGGTGACGGTGTCACGCACACTGTTCCAATCTACGAAGGCTACTCACTGCCCCATGCAATCCTCAGGCTGGACCTTGCCGGTCG
upper sequence: LOC_Os01g73310.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ17401 (Selaginella moellendorffii), 3'ss of exon 2
----------------------------------------ggtcagtaggtgttagaattat--attatctatgctcaataatagtcgtgcaatta-tttaatgttggtcagtgcatatggc--------taatgctgttttaatcaacagGTATTGTTCTGGACTCGGGTGATGGTGTGAGCCATACTGTTCCCATCTATGAAGGATATGCACTTCCTCATGCAATCCTTCGTCTGGATCTTGCTGGCCG
||| | ||||| || | || | | | | | | | | | || || | || || | | | | | | || || ||| | | ||||||||||||| ||||||||||| ||||| | || |||||||| ||||| ||||| || |||| || ||||||||||| | ||||| ||||| || ||
gtatggagtttttttatcccttgcttgttctagacaagatggttgatgcgtgtttcttttcttcgttgcttgcgatagacatgatgcttcaagttggttctacttttgtttttccctctaacacgttgtatgatcgtggtttg-tgatcagGTATTGTTCTCGACTCGGGTGACGGTGTCACGCACACTGTTCCAATCTACGAAGGCTACTCACTGCCCCATGCAATCCTCAGGCTGGACCTTGCCGGTCGMapped 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|112787042|gb|EE591942.1|EE591942EST: TGTTGCAATCCAAGCAGTGCTTTCACTCTATGCTAGTGGCCGAACAACAG GTATTGTTCTGGACTCGGGTGATGGTGTGAGCCATACTGTTCCCATCTATG
genomic: TGTTGCAATCCAAGCAGTGCTTTCACTCTATGCTAGTGGCCGAACAACAGgtatgtgatg ... taatcaacagGTATTGTTCTGGACTCGGGTGATGGTGTGAGCCATACTGTTCCCATCTATG
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:
69 (upstream exon),
75 (downstream exon)
Score:
40GAGAAAATGACACAGATTATGTTTGAGACGTTCAATGTTCCTGCCATGTATGTTGCAATCCAAGCAGTGCTTTCACTCTATGCTAGTGGCCGAACAACAGgtatgtgatg ... taatcaacagGTATTGTTCTGGACTCGGGTGATGGTGTGAGCCATACTGTTCCCATCTATGAAGGATATGCACTTCCTCATGCAATCCTTCGTCTGGATCTTGCTGGCCG
<
<
<
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgcaattatttaatgttggtcagtgcatatggctaatgctgttttaatcaacagGTATTGTTCTGGACTCGGGTGATGGTGTGAGCCATACTGTTCCCATCTATGAAGGATATGCACTTCCTCATGCAATCCTTCGTCTGGATCTTGCTGGCCG
ttttaat putative branch site (score: 40)
ctgtttt CT-rich tract
attatttaatgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggtcagtaggtgttagaattatattatctatgctcaataatagtcgtgcaattatttaatgttggtcagtgcatatggctaatgctgttttaatcaacagGTATTGTTCTGGACTCGGGTGATGGTGTGAGCCATACTGTTCCCATCTATGAAGGATATGCACTTCCTCATGCAATCCTTCGTCTGGATCTTGCTGGCCG
- - - - - - - - - - - - - tctatgc
- - - - - - - - - - - - - - - - - - - - - - cgtgcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgcata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgtt