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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtatttaatacttcatgtcctttattcagtttgataattatgaagtttgtatttaatacgtcttgtcctttatgcagcttgagaaattatcttctgattttttttttatttttggctttactgtgcagTCGGAATATCCAGCTCTCCCTTAGTGTTCTCCTTTTTGGTGTTGGAGTTGCAACTGTGACTGACCTGCAGCTTAATGCTGTGGGATCTGTCCTGTCTTTG

Basic information

species Oryza sativa
transcript LOC_Os01g07310.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g07310.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G116053_T01 (Zea mays), 3'ss of exon 4
gtttgtatttaatacttcatgtcctttattcagtttgataattatgaagtttgtatttaatacgtcttgtcctttatgcagcttgagaaattatcttctgattttttttttatttttggctttactgtgcagTCGGAATATCCAGCTCTCCCTTAGTGTTCTCCTTTTTGGTGTTGGAGTTGCAACTGTGACTGACCTGCAGCTTAATGCTGTGGGATCTGTCCTGTCTTTG
                                                |||||  |  ||||| || ||| || ||||||| |  | |   || | ||| || |||||         | | || |||||||| ||||||||| |||| ||||||||||| |||||| |||||||||| ||||||||||| ||||| ||||| || || | | |||||||||| |||||  | 
------------------------------------------------gtttgcttgcaatacatcatgtgctatatgcaggtctatagtataccatctaatctttttcac-----cgacattgctgtgcagCCGGAATATCAAGCTTTCCCTTAGTGTGCTCCTTCTTGGTGTTGGTGTTGCAACTGTAACTGATCTGCAACTCAACGTTATGGGATCTGTACTGTCCCTA

upper sequence: LOC_Os01g07310.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G081848_T05 (Zea mays), 3'ss of exon 4
gtttgtatttaatacttcatgtcctttattcagtttgataattatgaagtttgtatttaatacgtcttgtcctttatgcagcttgagaaattatcttctgattttttttttatttttggctttactgtgcagTCGGAATATCCAGCTCTCCCTTAGTGTTCTCCTTTTTGGTGTTGGAGTTGCAACTGTGACTGACCTGCAGCTTAATGCTGTGGGATCTGTCCTGTCTTTG
                        ||| |||||   || | ||   | |||||| | ||||||||| ||| ||||||| ||||  | ||  || | ||| || |||||        || | | ||||||||||||||| ||| |||| ||||||||||| |||||| |||||||||| ||||||||| | ||||| ||||| || ||   ||||||||||||  ||||  | 
-----------------------ttttcttcaggaagaaattt---aggtttgtttgtaatacgtcatgtgctttatggagctctataatataccatctaatctttttcac-----tgacct-actgtgcagTCGGAACATCAAGCTTTCCCTTAGTGTGCTCCTTCTTGGTGTTGGTGTTGCAACTATAACTGATCTGCAACTCAACCTTGTGGGATCTGTATTGTCCCTA

upper sequence: LOC_Os01g07310.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G081848_T01 (Zea mays), 3'ss of exon 4
gtttgtatttaatacttcatgtcctttattcagtttgataattatgaagtttgtatttaatacgtcttgtcctttatgcagcttgagaaattatcttctgattttttttttatttttggctttactgtgcagTCGGAATATCCAGCTCTCCCTTAGTGTTCTCCTTTTTGGTGTTGGAGTTGCAACTGTGACTGACCTGCAGCTTAATGCTGTGGGATCTGTCCTGTCTTTG
                                                |||||| | ||||||||| ||| ||||||| ||||  | ||  || | ||| || |||||        || | | ||||||||||||||| ||| |||| ||||||||||| |||||| |||||||||| ||||||||| | ||||| ||||| || ||   ||||||||||||  ||||  | 
------------------------------------------------gtttgtttgtaatacgtcatgtgctttatggagctctataatataccatctaatctttttcac-----tgacct-actgtgcagTCGGAACATCAAGCTTTCCCTTAGTGTGCTCCTTCTTGGTGTTGGTGTTGCAACTATAACTGATCTGCAACTCAACCTTGTGGGATCTGTATTGTCCCTA

Mapped 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|58657497|gb|CK046177.1|CK046177
EST:     ATCCCCTGCACTGTTATACTTGAGACTCTTTTCTTCAGGAAGAAGTTTAG                         TCGGAATATCCAGCTCTCCCTTAGTGTTCTCCTTTTTGGTGTTGGAGTT
genomic: ATCCCCTGCACTGTTATACTTGAGACTCTTTTCTTCAGGAAGAAGTTTAGgtttgtattt ... tactgtgcagTCGGAATATCCAGCTCTCCCTTAGTGTTCTCCTTTTTGGTGTTGGAGTT
EST: gi|58689272|gb|CK077959.1|CK077959
EST:     ATCCCCTGCACTGTTATACTTGAGACTCTTTTCTTCAGGAAGAAGTTTAG                         TCGGAATATCCAGCTCTCCCTTAGTGTTCTCCT
genomic: ATCCCCTGCACTGTTATACTTGAGACTCTTTTCTTCAGGAAGAAGTTTAGgtttgtattt ... tactgtgcagTCGGAATATCCAGCTCTCCCTTAGTGTTCTCCT
EST: gi|33679023|gb|CF307262.1|CF307262
EST:     ATCCCCTGCACTGTTATACTTGAGACTCTTTTCTTCAGGAAGAAGTTTAG                         TCGGAATATCCAGCTCTCCCTTAGTGTTCTCCTTTTTGGTGTTGGAGTTGC
genomic: ATCCCCTGCACTGTTATACTTGAGACTCTTTTCTTCAGGAAGAAGTTTAGgtttgtattt ... tactgtgcagTCGGAATATCCAGCTCTCCCTTAGTGTTCTCCTTTTTGGTGTTGGAGTTGC
EST: gi|33679263|gb|CF307502.1|CF307502
EST:     ATCCCCTGCACTGTTATACTTGAGACTCTTTTCTTCAGGAAGAAGTTTAG                         TCGGAATATCCAGCTCTCCCTTAGTGTTCTCCTTTTTGGTGTTGGAGTTGC
genomic: ATCCCCTGCACTGTTATACTTGAGACTCTTTTCTTCAGGAAGAAGTTTAGgtttgtattt ... tactgtgcagTCGGAATATCCAGCTCTCCCTTAGTGTTCTCCTTTTTGGTGTTGGAGTTGC
EST: gi|29646078|gb|CB651085.1|CB651085
EST:     ATCCCCTGCACTGTTATACTTGAGACTCTTTTCTTCAGGAAGAAGTTTAG                         TCGGAATATCCAGCTCTCCCTTAGTGGTCTCCTTTTTGGAGTAGGAGTTGC
genomic: ATCCCCTGCACTGTTATACTTGAGACTCTTTTCTTCAGGAAGAAGTTTAGgtttgtattt ... tactgtgcagTCGGAATATCCAGCTCTCCCTTAGTGTTCTCCTTTTTGGTGTTGGAGTTGC
EST: gi|218500395|gb|FG958811.1|FG958811
EST:     ATCCCCTGCACTGTTATACTTGAGACTCTTTTCTTCAGGAAGAAGTTTAG                         TCGGAATATCCAGCTCTCCCTTAGTGTTCTCCTTTTTGGTGTTGGAGTTGC
genomic: ATCCCCTGCACTGTTATACTTGAGACTCTTTTCTTCAGGAAGAAGTTTAGgtttgtattt ... tactgtgcagTCGGAATATCCAGCTCTCCCTTAGTGTTCTCCTTTTTGGTGTTGGAGTTGC
EST: gi|58693672|gb|CK082359.1|CK082359
EST:     ATCCCCTGCACTGTTATACTTGAGACTCTTTTCTTCAGGAAGAAGTTTAG                         TCGGAATATCCAGCTCTCCCTTAGTGTTCTCCTTTTTGGTGTTGGAGTTGC
genomic: ATCCCCTGCACTGTTATACTTGAGACTCTTTTCTTCAGGAAGAAGTTTAGgtttgtattt ... tactgtgcagTCGGAATATCCAGCTCTCCCTTAGTGTTCTCCTTTTTGGTGTTGGAGTTGC
EST: gi|58691484|gb|CK080171.1|CK080171
EST:     ATCCCCTGCACTGTTATACTTGAGACTCTTTTCTTCAGGAAGAAGTTTAG                         TCGGAATATCCAGCTCTCCCTTAGTGTTCTCCTTTTTGGTGTTGGAGTTGC
genomic: ATCCCCTGCACTGTTATACTTGAGACTCTTTTCTTCAGGAAGAAGTTTAGgtttgtattt ... tactgtgcagTCGGAATATCCAGCTCTCCCTTAGTGTTCTCCTTTTTGGTGTTGGAGTTGC
EST: gi|29666174|gb|CB662449.1|CB662449
EST:     ATCCCCTGCACTGTTATACTTGAGACTCTTTTCTTCAGGAAGAAGTTTAG                         TCGGAATATCCAGCTCTCCCTTAGTGTTCTCCTTTTTGGTGTTGGAGTTGC
genomic: ATCCCCTGCACTGTTATACTTGAGACTCTTTTCTTCAGGAAGAAGTTTAGgtttgtattt ... tactgtgcagTCGGAATATCCAGCTCTCCCTTAGTGTTCTCCTTTTTGGTGTTGGAGTTGC
EST: gi|218479998|gb|FG959805.1|FG959805
EST:     ATCCCCTGCACTGTTATACTTGAGACTCTTTTCTTCAGGAAGAAGTTTAG                         TCGGAATATCCAGCTCTCCCTTAGTGTTCTCCTTTTTGGTGTTGGAGTTGC
genomic: ATCCCCTGCACTGTTATACTTGAGACTCTTTTCTTCAGGAAGAAGTTTAGgtttgtattt ... tactgtgcagTCGGAATATCCAGCTCTCCCTTAGTGTTCTCCTTTTTGGTGTTGGAGTTGC
EST: gi|2796302|gb|AA749596.1|AA749596
EST:     ATCCCCTGCACTGTTATACTTGAGACTCTTTTCTTCAGGAAGAAGTTTAG                         TCGGAATATCCAGCTCTCCCTTTCAGTGTTCTCCTTT
genomic: ATCCCCTGCACTGTTATACTTGAGACTCTTTTCTTCAGGAAGAAGTTTAGgtttgtattt ... tactgtgcagTCGGAATATCCAGCTCTCCCTT--AGTGTTCTCCTTT
EST: gi|58665638|gb|CK054324.1|CK054324
EST:     ATCCCCTGCACTGTTATACTTGAGACTCTTTTCTTCAGGAAGAAGTTTAG                         TCGGAATATCCAGCTCTCCCTTAGTGTTCTCCTTTTTGGTGTTGGAGTTGC
genomic: ATCCCCTGCACTGTTATACTTGAGACTCTTTTCTTCAGGAAGAAGTTTAGgtttgtattt ... tactgtgcagTCGGAATATCCAGCTCTCCCTTAGTGTTCTCCTTTTTGGTGTTGGAGTTGC
EST: gi|58686479|gb|CK075166.1|CK075166
EST:     ATCCCCTGCACTGTTATACTTGAGACTCTTTTCTTCAGGAAGAAGTTTAG                         TCGGAATATCCAGCTCTCCCTTAGT
genomic: ATCCCCTGCACTGTTATACTTGAGACTCTTTTCTTCAGGAAGAAGTTTAGgtttgtattt ... tactgtgcagTCGGAATATCCAGCTCTCCCTTAGT
EST: gi|29663298|gb|CB659573.1|CB659573
EST:     ATCCCCTGCACTGTTATACTTGAGACTCTTTTCTTCAGGAAGAAGTTTAG                         TCGGAATATCCAGCTCTCCCTTAGTGTTCTCCTTTTTGGTGTTGGAGTTGC
genomic: ATCCCCTGCACTGTTATACTTGAGACTCTTTTCTTCAGGAAGAAGTTTAGgtttgtattt ... tactgtgcagTCGGAATATCCAGCTCTCCCTTAGTGTTCTCCTTTTTGGTGTTGGAGTTGC
EST: gi|29645083|gb|CB650090.1|CB650090
EST:     ATCCCCTGCACTGTTATACTTGAGACTCTTTTCTTCAGGAAGAAGTTTAG                         TCGGAATATCCAGCTCTCCCTTAGTGTTCTCCTTTTTGGTGTTGGAGTTGC
genomic: ATCCCCTGCACTGTTATACTTGAGACTCTTTTCTTCAGGAAGAAGTTTAGgtttgtattt ... tactgtgcagTCGGAATATCCAGCTCTCCCTTAGTGTTCTCCTTTTTGGTGTTGGAGTTGC
EST: gi|29641313|gb|CB646320.1|CB646320
EST:     ATCCCCTGCACTGTTATACTTGAGACTCTTTTCTTCAGGAAGAAGTTTAG                         TCGGAATATCCAGCTCTCCCTTAGTGTTCTCCTTTTTGGTGTTGGAGTTGC
genomic: ATCCCCTGCACTGTTATACTTGAGACTCTTTTCTTCAGGAAGAAGTTTAGgtttgtattt ... tactgtgcagTCGGAATATCCAGCTCTCCCTTAGTGTTCTCCTTTTTGGTGTTGGAGTTGC
EST: gi|29645955|gb|CB650962.1|CB650962
EST:     ATCCCCTGCACTGTTATACTTGAGACTCTTTTCTTCAGGAAGAAGTTTAG                         TCGGAATATCCAGCTCTCCCTTAGTGTTCTCCTTTTTGGTGTTGGAGTTGC
genomic: ATCCCCTGCACTGTTATACTTGAGACTCTTTTCTTCAGGAAGAAGTTTAGgtttgtattt ... tactgtgcagTCGGAATATCCAGCTCTCCCTTAGTGTTCTCCTTTTTGGTGTTGGAGTTGC
EST: gi|58687536|gb|CK076223.1|CK076223
EST:     ATCCCCTGCACTGTTATACTTGAGACTCTTTTCTTCAGGAAGAAGTTTAG                         TCGGAATATCCAGCTCTCCCTTAGTGTTCTCCTTTTTGGTGTTGGAGTTGC
genomic: ATCCCCTGCACTGTTATACTTGAGACTCTTTTCTTCAGGAAGAAGTTTAGgtttgtattt ... tactgtgcagTCGGAATATCCAGCTCTCCCTTAGTGTTCTCCTTTTTGGTGTTGGAGTTGC
EST: gi|428121|gb|D24269.1|D24269
EST:     CTTTTCTTCAGGAAGNAGTTTAG                         TCGGAATATCCAGCTCTCCCTTAGTGTTCTCCTTTTTGGTGTTGGAGTTGC
genomic: CTTTTCTTCAGGAAGAAGTTTAGgtttgtattt ... tactgtgcagTCGGAATATCCAGCTCTCCCTTAGTGTTCTCCTTTTTGGTGTTGGAGTTGC
EST: gi|33796589|gb|CF324162.1|CF324162
EST:     ATCCCCTGCACTGTTATACTTGAGACTCTTTTCTTCAGGAAGAAGTTTAG                         TCGGAATATCCAGCTCTCCCTTAGTGTTCTCCTTTTTGGTGTTGGAGTTGC
genomic: ATCCCCTGCACTGTTATACTTGAGACTCTTTTCTTCAGGAAGAAGTTTAGgtttgtattt ... tactgtgcagTCGGAATATCCAGCTCTCCCTTAGTGTTCTCCTTTTTGGTGTTGGAGTTGC
EST: gi|29681211|gb|CB677486.1|CB677486
EST:     ATCCCCTGCACTGTTATACTTGAGACTCTTTTCTTCAGGAAGAAGTTTAG                         TCGGAATATCCAGCTCTCCCTTAGTGTTCTCCTTTTTGGTGTTGGAGTTGC
genomic: ATCCCCTGCACTGTTATACTTGAGACTCTTTTCTTCAGGAAGAAGTTTAGgtttgtattt ... tactgtgcagTCGGAATATCCAGCTCTCCCTTAGTGTTCTCCTTTTTGGTGTTGGAGTTGC
EST: gi|86899011|gb|CI296202.1|CI296202
EST:     ATCCCCTGCACTGTTATACTTGAGACTCTTTTCTTCAGGAAGAAGTTTAG                         TCGGAATATCCAGCTCTCCCTTAGTGTTCTCCTTTTTGGTGTTGGAGTTGC
genomic: ATCCCCTGCACTGTTATACTTGAGACTCTTTTCTTCAGGAAGAAGTTTAGgtttgtattt ... tactgtgcagTCGGAATATCCAGCTCTCCCTTAGTGTTCTCCTTTTTGGTGTTGGAGTTGC

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: 58 (upstream exon), 68 (downstream exon)
Score: 51

ATGACAAAGCTGGCAATTATCCCCTGCACTGTTATACTTGAGACTCTTTTCTTCAGGAAGAAGTTTAGgtttgtattt ... tactgtgcagTCGGAATATCCAGCTCTCCCTTAGTGTTCTCCTTTTTGGTGTTGGAGTTGCAACTGTGACTGACCTGCAGCTTAATGCTGTGGGATCTGTCCTGTCTTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcagcttgagaaattatcttctgattttttttttatttttggctttactgtgcagTCGGAATATCCAGCTCTCCCTTAGTGTTCTCCTTTTTGGTGTTGGAGTTGCAACTGTGACTGACCTGCAGCTTAATGCTGTGGGATCTGTCCTGTCTTTG
                  ttctgat  putative branch site (score: 51)
                        ttttttttttattttt  CT-rich tract
     ttgagaaattatcttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtatttaatacttcatgtcctttattcagtttgataattatgaagtttgtatttaatacgtcttgtcctttatgcagcttgagaaattatcttctgattttttttttatttttggctttactgtgcagTCGGAATATCCAGCTCTCCCTTAGTGTTCTCCTTTTTGGTGTTGGAGTTGCAACTGTGACTGACCTGCAGCTTAATGCTGTGGGATCTGTCCTGTCTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG