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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agttataataaatcacctgtgttattagtctgatcactaacttaagtgctcttgtttatatgctgatcctgatagttgctttttcttgttttgttttcagGTGGCTGACTCACTTGAGAAAGGAACAGAACATGAGGATGAATACATGATTAGTGAAAAGGAGCTTCTTGTTAACCG

Basic information

species Oryza sativa
transcript LOC_Os01g51220.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g51220.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G439457_T01 (Zea mays), 3'ss of exon 5
------agttataataaatcacctgtgttattagtctgatcactaacttaagtgctcttgtttatatgctgatcctgatagttgctttttcttgttttgttttcagGTGGCTGACTCACTTGAGAAAGGAACAGAACATGAGGATGAATACATGATTAGTGAAAAGGAGCTTCTTGTTAACCG-----------------------
           |||    | ||||| | ||||  | | |||||| |  |  || | | || || | |  | || ||| |||||||||| |  ||         |||||||||||||||||||| || ||||||||||| ||||||||||||||||| ||||||||||||||||||||||||||                       
atggttgacggtaaatgttaacctgcgatattctttttatcactgaacttcgttcacatgattgtttcttaattctggtagttgctttattatgaac------cagGTGGCTGACTCACTTGAAAAGGGAACAGAACACGAGGATGAATACATGATCAGTGAAAAGGAGCTTCTTGTTAACCGGTTTGTGAACTTGTGTACTTCAT

upper sequence: LOC_Os01g51220.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G439457_T02 (Zea mays), 3'ss of exon 5
------agttataataaatcacctgtgttattagtctgatcactaacttaagtgctcttgtttatatgctgatcctgatagttgctttttcttgttttgttttcagGTGGCTGACTCACTTGAGAAAGGAACAGAACATGAGGATGAATACATGATTAGTGAAAAGGAGCTTCTTGTTAACCG
           |||    | ||||| | ||||  | | |||||| |  |  || | | || || | |  | || ||| |||||||||| |  ||         |||||||||||||||||||| || ||||||||||| ||||||||||||||||| ||||||||||||||||||||||||||
atggttgacggtaaatgttaacctgcgatattctttttatcactgaacttcgttcacatgattgtttcttaattctggtagttgctttattatgaac------cagGTGGCTGACTCACTTGAAAAGGGAACAGAACACGAGGATGAATACATGATCAGTGAAAAGGAGCTTCTTGTTAACCG

upper sequence: LOC_Os01g51220.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA18G03480.1 (Glycine max), 3'ss of exon 5
agttataataaatcacct--gtgttattagtctgatcactaacttaagtgctcttgtttatatgctgatcctgata-gttgctttttcttgttttgttttcagGTGGCTGACTCACTTGAGAAAGGAACAGAACATGAGGATGAATACATGATTAGTGAAAAGGAGCTTCTTGTTAACCG-
    ||| |   |   ||  |  |   ||   |  |||   |  | | |  | | |    |       |    ||   ||| ||||| ||  | |  | | |||| ||||| ||||| ||||||||||| |||||||| |||||||||||||| |||||||||||||| || || |||   
----atactcgtttttcttggaatgtgtaaagttgtcagctatcttaatattttagcagctccctaagtttcaatgtattgttttttatttgtcttatattaggTAGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTAGTAAACAAG

upper sequence: LOC_Os01g51220.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA11G34840.1 (Glycine max), 3'ss of exon 5
agttataat--aaatcacctgtgttattagtctgatcactaacttaagtgctcttgtttatatgctgatcctgatagttgctttttcttgttt---tgttttcagGTGGCTGACTCACTTGAGAAAGGAACAGAACATGAGGATGAATACATGATTAGTGAAAAGGAGCTTCTTGTTAACCG
 ||| |  |   |||       ||| | |  ||    |||| ||||| |  | ||         || |   | | | ||  ||||  || |||   |  | | |||| ||||| ||||| ||||||||||| |||||||| |||||||||||||| |||||||||||||| || || |||  
-gttttccttggaatgtggaaagttgtcaa-ctatctactatcttaatt--ttttagcagctccctaagtttca-acttatttttatttatttatctaatattagGTTGCTGATTCACTGGAGAAAGGAACTGAACATGAAGATGAATACATGATCAGTGAAAAGGAGCTCCTCGTAAACAA

upper sequence: LOC_Os01g51220.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT5G58030.1 (Arabidopsis thaliana), 3'ss of exon 4
agttataataaatcacctgtgttattagtctgatcactaacttaagtgctcttgtttatatgc-tgatcctg-atagttgctttttcttgttttgttttc---agGTGGCTGACTCACTTGAGAAAGGAACAGAACATGAGGATGAATACATGATTAGTGAAAAGGAGCTTCTTGTTAACCG
        | | |  |     ||   | |   || | |   || |||| |  | |  | |||| || ||||| ||  |  ||    |||        | |   |||| ||||| |||||||| ||||||||||||||||| ||||| |||||||| |||||||||||||||||||||||| |
-------gtgagtggc---gatttcaaattcaattagttg-ttgagtgtttctatcgacatgcctgttcctggattctaactcacacttaacgaacatgccatagGTTGCTGATTCACTTGAAAAAGGAACAGAACATGAAGATGAGTACATGATCAGTGAAAAGGAGCTTCTTGTTAACAG

upper sequence: LOC_Os01g51220.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv11s0037g00110.t01 (Vitis vinifera), 3'ss of exon 4
-agttataataaatcacctgtgttattagtctgatcactaacttaagtgctcttgttta-tatgctgatcctgatagttgctttttcttgttttgttttcagGTGGCTGACTCACTTGAGAAAGGAACAGAACATGAGGATGAATACATGATTAGTGAAAAGGAGCTTCTTGTTAACCG
  |  ||| |   |||  | |||||  ||     | |  || ||   |  |    |  | |      ||| | ||  ||  || |  ||| | |  | | |||| |||||||||||||||||||| || || || || |||||||||||||| ||||| || ||||| || |||||  |
tggccatacttcttcatttctgttaaaagaggcctgatgaatttttatcatgccatgaaatgcagccatctttatcatt--ttctatttgatatcatattagGTAGCTGACTCACTTGAGAAAGGTACTGAGCACGAAGATGAATACATGATCAGTGAGAAAGAGCTCCTGGTTAATAG

upper sequence: LOC_Os01g51220.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S303_47V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------------agttataataaatcacctgtgttattagtctgatcactaacttaagtg-ctcttgtttatatg--ctgatcctgatagttgctttttcttgttttgttttcagGTGGCTGACTCACTTGAGAAAGGAACAGAACATGAGGATGAATACATGATTAGTGAAAAGGAGCTTCTTGTTAACCG
                             | | |||  |     ||||    ||| |  ||||  |  ||| || |||    | || |    | ||  || |   |  | | | |||| ||    ||||||||| || ||  | || || || || |||||||| ||||| |||||||| ||||| |||||||||||||||||| |
gtttttaacttggcccttacgatcgagcctctgatagtttg---gtgtctcaagttttctcac--atgtaattgactcgcactaatgtcatttcattttgtttcattttatattttgtattacactcagGTGGCAGATTCTTTAGAAAAGGGCACGGAACATGAAGATGAGTACATGATCAGTGAGAAGGAGCTTCTTGTTAACAG

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|88347620|gb|CI634305.1|CI634305
EST:     GTATATTATCGTTCACTCACAGCACTGTATGGAAAGNTTGGTTGGGGAAG                         GTGGCTGACTCACT
genomic: GTATATTATCGTTCATTCACAGCACTGTATGGAAAGTTTTGTTTGGGAAGgtactgtgtt ... ttgttttcagGTGGCTGACTCACT
EST: gi|87031904|gb|CI268133.1|CI268133
EST:     GTATATTATCGTTCATTCACAGCACTGTATGGAAAGTTTTGTTTGGGAAG                         GTGGCTGACTCACTTGAGAAAGGAACAGAACATGAGGATGAATACATGATT
genomic: GTATATTATCGTTCATTCACAGCACTGTATGGAAAGTTTTGTTTGGGAAGgtactgtgtt ... ttgttttcagGTGGCTGACTCACTTGAGAAAGGAACAGAACATGAGGATGAATACATGATT
EST: gi|88243947|gb|CI243069.1|CI243069
EST:     TTCACAGCACTGTATGGAAAGTTTTGTTTGGGAAG                         GTGGCTGACTCACTTGAGAAAGGAACAGAACATGAGGATGAATACATGATT
genomic: TTCACAGCACTGTATGGAAAGTTTTGTTTGGGAAGgtactgtgtt ... ttgttttcagGTGGCTGACTCACTTGAGAAAGGAACAGAACATGAGGATGAATACATGATT
EST: gi|109974426|gb|DT806902.1|DT806902
EST:     GTATATTATCGGTCATTCACAGCACTGTATGGAAAGTTTTGTTTGGGAAG                         GTGGCTGACTCACTTGAGAAAGGAACAGAACATGAGGATGAATACATGATT
genomic: GTATATTATCGTTCATTCACAGCACTGTATGGAAAGTTTTGTTTGGGAAGgtactgtgtt ... ttgttttcagGTGGCTGACTCACTTGAGAAAGGAACAGAACATGAGGATGAATACATGATT
EST: gi|88575793|gb|CI669938.1|CI669938
EST:     GTATATTATCGTTCATCCACAGCACTGTATGGAAAGTTTTGTTTGGGAAG                         GTGGCTGACTCACTTGAGAAAGGAA
genomic: GTATATTATCGTTCATTCACAGCACTGTATGGAAAGTTTTGTTTGGGAAGgtactgtgtt ... ttgttttcagGTGGCTGACTCACTTGAGAAAGGAA
EST: gi|163929185|gb|EG713058.1|EG713058
EST:     GTATATTATCGTTCATTCACAGCACTGTATGGAAAGTTTTGTTTGGGAAG                         GTGGCTGACTCACTTGAGAAAGGAACAGAACATGAGGATGAATACATGATT
genomic: GTATATTATCGTTCATTCACAGCACTGTATGGAAAGTTTTGTTTGGGAAGgtactgtgtt ... ttgttttcagGTGGCTGACTCACTTGAGAAAGGAACAGAACATGAGGATGAATACATGATT
EST: gi|88381600|gb|CI682265.1|CI682265
EST:     GTATATTATCGTTCATTCACAGCACTGTATGGAAAGTTTTGGTTGGGAAG                         GTGGCTGACTCACTTGACAAAGGAACAGAACA
genomic: GTATATTATCGTTCATTCACAGCACTGTATGGAAAGTTTTGTTTGGGAAGgtactgtgtt ... ttgttttcagGTGGCTGACTCACTTGAGAAAGGAACAGAACA

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: 71 (upstream exon), 74 (downstream exon)
Score: 48

GGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATTCACAGCACTGTATGGAAAGTTTTGTTTGGGAAGgtactgtgtt ... ttgttttcagGTGGCTGACTCACTTGAGAAAGGAACAGAACATGAGGATGAATACATGATTAGTGAAAAGGAGCTTCTTGTTAACCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgctcttgtttatatgctgatcctgatagttgctttttcttgttttgttttcagGTGGCTGACTCACTTGAGAAAGGAACAGAACATGAGGATGAATACATGATTAGTGAAAAGGAGCTTCTTGTTAACCG
                     tcctgat  putative branch site (score: 48)
                              ttgctttttcttgttt  putative PPT
      ttgtttatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agttataataaatcacctgtgttattagtctgatcactaacttaagtgctcttgtttatatgctgatcctgatagttgctttttcttgttttgttttcagGTGGCTGACTCACTTGAGAAAGGAACAGAACATGAGGATGAATACATGATTAGTGAAAAGGAGCTTCTTGTTAACCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - -cacctgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgat