Sequence
atgc intronic sequence ATGC exonic sequencegtaagtgtctgtcctttaagctctctggtgcccttttatggatctaattttcgtcatgtacagGATACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAATG
Basic information
species | Oryza sativa |
transcript | LOC_Os04g59494.4 |
intron # | 25 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g59494.1 (Oryza sativa), 3'ss of exon 25
lower sequence: GRMZM2G376731_T01 (Zea mays), 3'ss of exon 25
---------------------------------------------------gtaagtgtctgtcctttaagctct---ctggtgccctttta-tggatctaattttcgtcatgta---cagGATACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAATG
| || || | ||| | || | || ||| | |||| || ||| | ||| |||||| |||||||||||||||||||||| || || ||||| || |||||||||
gtaagtgccccctctttttttccctggacccgaagggttagagaaggaaggatgggtttcaggtgttttatctatggtttgttgcatgacgaatggaacttgtttctttggtgtgaaccagGATCAGAGATGATTTTGAGAAAGAGGACGCGTTTCATGGACTGTGTGCAATG
upper sequence: LOC_Os04g59494.1 (Oryza sativa), 3'ss of exon 25
lower sequence: GLYMA10G42960.1 (Glycine max), 3'ss of exon 25
---------------------------------gtaagtgtctgtcctttaagctctctggtgcccttttatg--gatctaattttc----gtcatgtacagGATACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAATG
|| |||| ||| | | ||||| ||| ||| |||| ||| || | | |||||||||||||||| |||||||||||||||| || ||||||||||| |||
atctcaacatcactttacaaattgaccataatattagatgtccactgtttca--ttgctggttatcttgtatattaatctctctttgatgggttttttgcagGATACGAGATGATGTTGAGAAAGAGGATGCTTTTAGAGGTCTATGTGCTATG
upper sequence: LOC_Os04g59494.1 (Oryza sativa), 3'ss of exon 25
lower sequence: GLYMA20G24040.1 (Glycine max), 3'ss of exon 25
----------------------------------gtaagtgtctgtcctttaagctctctggtgcccttttatg--gatctaattttcgtcatgt---acagGATACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAATG
|| |||| ||| | | ||||| ||| ||| || | ||| | || | |||||||||||||||| |||||||||||||||| || ||||||||||| |||
ctcaacctcttcactttacaaattgatcataatattagatgtccactgtttca--ttgctggttatcttgtatattaatttctctttgatgattttttgcagGATACGAGATGATGTTGAGAAAGAGGATGCTTTTAGAGGTCTATGTGCTATG
upper sequence: LOC_Os04g59494.1 (Oryza sativa), 3'ss of exon 25
lower sequence: Vv18s0001g00910.t01 (Vitis vinifera), 3'ss of exon 25
----------------------------gtaagtgtctgtcctttaagctct--ctggtgcccttttatggatctaat--tttcgtcatgt-----acagGATACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAATG
| | || | | ||| | | | | ||||| | | | | | || || ||||||||| |||||| ||||||| || ||||| |||| ||||||||||||||
attggactcatactaccttttacatatgccataactttgcctgctgagcacaggcccattcttttttaacagttcattaataccaacaagttcatggcagGATACGTGATGATATTGAGAAGGAAGATGCCTTCCGTGGTCTATGTGCAACT
upper sequence: LOC_Os04g59494.1 (Oryza sativa), 3'ss of exon 25
lower sequence: PP1S276_77V6.1 (Physcomitrella patens), 3'ss of exon 25
--------------------------------gtaagtgtctgtcctttaa--gctctctggtgccc-ttttatggatctaattttcgtcatgtac--agGATACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAATG
| | | | ||| | | ||| | || | ||||| ||| |||| | | | | |||||||||||||||||||||||||| ||||| || | || || ||||| |||
gtatctattttgttacttgttcaatctcttcaacttggttttaccgtttgatcgttctttcgtatcagttttaaactactattttttcttttcttctcagGATACGAGATGATTTTGAGAAAGAAGATGCTTTTCGAGGCCTGTGTGCTATG
upper sequence: LOC_Os04g59494.1 (Oryza sativa), 3'ss of exon 25
lower sequence: PP1S41_175V6.1 (Physcomitrella patens), 3'ss of exon 24
------------------------------gtaagtgtc-tgtcctttaagctctctggtgccctt--ttatg--gatctaattttcgtcatg--tacagGATACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAATG
|| || | || | ||| || | | || | ||| | || | | || || | |||||||||||||||||||||||| || |||||||||| || | ||||| |||
gtttttgaggttgtgtttgaggttgtttgcgtttgtatgatgataatgaagaagtcagtcccttttactcatgatgcactgaaatatatcttgcttgcagGATACGAGATGATTTTGAGAAGGAAGATGCATTCCGGGGCTTGTGTGCCATG
upper sequence: LOC_Os04g59494.1 (Oryza sativa), 3'ss of exon 25
lower sequence: PP1S14_82V6.1 (Physcomitrella patens), 3'ss of exon 25
----------------------------------gtaagtgtctgtcctttaagctctctggtgccc--ttttatggatctaattttcgtcatgt-acagGATACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAATG
| || ||| | | | | | | | ||| | | | |||| || | ||||||||||||||||||||||||| || ||||| || | || | ||||| |||
tataataattagaaacttgctcaacctcttatattttggtatctaatttgtttgttttttaatataagatttcaaacactcactttttttctcttcacagGATACGAGATGATTTTGAGAAGGAAGATGCTTTTCGAGGATTGTGTGCTATGMapped 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|58608072|gb|CK036105.1|CK036105EST: GCCCCCCACATGGACCATTTCATGCAAGCCTGGTGCAATGCCTTGTGCAT GATACGAGATGATTTTGAGAA
genomic: GCCCCCCACATGGACCATTTCATGCAAGCCTGGTGCAATGCCTTGTGCATgtaagtgtct ... tcatgtacagGATACGAGATGATTTTGAGAA
EST:
gi|29669949|gb|CB666224.1|CB666224EST: GCCCCCCACATGGACCATTTCATGCAAGCCTGGTGCAATGCCTTGTGCAT GATACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAAT
genomic: GCCCCCCACATGGACCATTTCATGCAAGCCTGGTGCAATGCCTTGTGCATgtaagtgtct ... tcatgtacagGATACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAAT
EST:
gi|29624709|gb|CB629720.1|CB629720EST: TTCATGCAAGCCTGGTGCAATGCCTTGTGCAT GATACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAAT
genomic: TTCATGCAAGCCTGGTGCAATGCCTTGTGCATgtaagtgtct ... tcatgtacagGATACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAAT
EST:
gi|86437650|gb|CI119570.1|CI119570EST: GGTGCAATGCCTTGTGCAT GATACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAAT
genomic: GGTGCAATGCCTTGTGCATgtaagtgtct ... tcatgtacagGATACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAAT
EST:
gi|66929408|gb|CX116256.1|CX116256EST: GCCCCCACATGGGACCATTTCATGCAAGCCTGGTGCAATGCCTTGTGCAT GATACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAAT
genomic: CCCCCCACATGG-ACCATTTCATGCAAGCCTGGTGCAATGCCTTGTGCATgtaagtgtct ... tcatgtacagGATACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAAT
EST:
gi|58592654|gb|CF990962.1|CF990962EST: GCCCCCCACATGGACCATTTCATGCAAGCCTGGTGCAATGCCTTGTGCAT GATACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAAT
genomic: GCCCCCCACATGGACCATTTCATGCAAGCCTGGTGCAATGCCTTGTGCATgtaagtgtct ... tcatgtacagGATACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAAT
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:
75 (upstream exon),
52 (downstream exon)
Score:
27ATAGCGCAATCACTCTTGGGAGGCTTTGCTGGGTCTGTCCAGACATTGTGGCCCCCCACATGGACCATTTCATGCAAGCCTGGTGCAATGCCTTGTGCATgtaagtgtct ... tcatgtacagGATACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAATG
<
<
<
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgtcctttaagctctctggtgcccttttatggatctaattttcgtcatgtacagGATACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAATG
atctaat putative branch site (score: 27)
ttttcgtc CT-rich tract
atctaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtgtctgtcctttaagctctctggtgcccttttatggatctaattttcgtcatgtacagGATACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG