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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgttattgaggagtactcatatttattgttccagtgggtatacagaagttgtagataccgtagtaaaatactccattctgcaatcacagGTGCAGAAGCTGGTTGAGATGGGCTTCCCTGAAGACATGGTGAGAAGTGTTCTGAAGAGTGTCAATGGCGACGAGAACATGGCTCTTGAGAAGCTCTGCT

Basic information

species Oryza sativa
transcript LOC_Os01g70140.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g70140.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G134176_T01 (Zea mays), 3'ss of exon 4
gtattgttattgaggagtactcatatttattgttccagtgggtatacagaagttgtagataccgtagtaaaatactccattctgcaatcacagGTGCAGAAGCTGGTTGAGATGGGCTTCCCTGAAGACATGGTGAGAAGTGTTCTGAAGAGTGTCAATGGCGACGAGAACATGGCTCTTGAGAAGCTCTGCT
||||||  |     |   |        |  || | || |   |       ||  |  |  |||    |    |  | || |    |    |||||||||||||||||||||||||||||||| || ||   |||||||||||  |||||||| ||  |||||||||||||||||||||| || ||||||||||
gtattgcgagcactgttcatcatcccattgtgatacattccatgcttgccagcggcggtcaccaccctctgtt--tgcacttgttatctgcagGTGCAGAAGCTGGTTGAGATGGGCTTCCCAGAGGATCAGGTGAGAAGTGCCCTGAAGAGCGTGGATGGCGACGAGAACATGGCTCTCGAAAAGCTCTGCT
















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|86425727|gb|CI070824.1|CI070824
EST:     ACTGGACGGAGGCCTTTGCAAAGAATTCCTCCACCGGCATGGAAGAAAAG                         GTGCAGAAGCTGGTTGAGATGGGCTTCCCTGAAGACATGTTGAGAAGTGTT
genomic: ACTGGACGGAGGCCTTTGCAAAGAATTCCTCCACCGGCATGGAAGAAAAGgtattgttat ... gcaatcacagGTGCAGAAGCTGGTTGAGATGGGCTTCCCTGAAGACATGGTGAGAAGTGTT
EST: gi|88203348|gb|CI203197.1|CI203197
EST:     ACTGGGCGGAGGCCTTTGCAAAGAATTCCTCCACCGGCATGGAAGAAAAG                         GTGCAGAAGCTGGTTGAGATGGGCTTCCCTGAAGACATGGTGAGAAGTGTT
genomic: ACTGGACGGAGGCCTTTGCAAAGAATTCCTCCACCGGCATGGAAGAAAAGgtattgttat ... gcaatcacagGTGCAGAAGCTGGTTGAGATGGGCTTCCCTGAAGACATGGTGAGAAGTGTT
EST: gi|86529021|gb|CI169227.1|CI169227
EST:     ACTGGACGGAGGCCTTTGCAAAGAATTCCTCCACCGGCATGGAAGAAAAG                         GTGCAGAAGCTGGTTGAGATGGGCTTCCCTGAAGACATGGTGAGAAGTGTT
genomic: ACTGGACGGAGGCCTTTGCAAAGAATTCCTCCACCGGCATGGAAGAAAAGgtattgttat ... gcaatcacagGTGCAGAAGCTGGTTGAGATGGGCTTCCCTGAAGACATGGTGAGAAGTGTT
EST: gi|88239054|gb|CI240216.1|CI240216
EST:     ACTGGACGGAGGCCTTTGCAAAGAATTCCTCCACCGGCATGGAAGAAAAG                         GTGCAGAAGCTGGTTGAGATGGGCTTCCCTGAAGACATGGTGAGAAGTGTT
genomic: ACTGGACGGAGGCCTTTGCAAAGAATTCCTCCACCGGCATGGAAGAAAAGgtattgttat ... gcaatcacagGTGCAGAAGCTGGTTGAGATGGGCTTCCCTGAAGACATGGTGAGAAGTGTT
EST: gi|87035145|gb|CI189767.1|CI189767
EST:     ACTGGACGGAGGCCTTTGCAAAGAATTCCTCCACCGGCATGGAAGAAAAG                         GTGCAGAAGCTGGTTGAGATGGGCTTCCCTGAAGACATGGTGAGAAGTGTT
genomic: ACTGGACGGAGGCCTTTGCAAAGAATTCCTCCACCGGCATGGAAGAAAAGgtattgttat ... gcaatcacagGTGCAGAAGCTGGTTGAGATGGGCTTCCCTGAAGACATGGTGAGAAGTGTT
EST: gi|86850828|gb|CI338804.1|CI338804
EST:     ACTGGACGGAGGCCTTTGCAAAGAATTCCTCCACCGGCATGGAAGAAAAG                         GTGCAGAAGCTGGTTGAGATGGGCTTCCCTGAAGACATGGTGAGAAGTGTT
genomic: ACTGGACGGAGGCCTTTGCAAAGAATTCCTCCACCGGCATGGAAGAAAAGgtattgttat ... gcaatcacagGTGCAGAAGCTGGTTGAGATGGGCTTCCCTGAAGACATGGTGAGAAGTGTT
EST: gi|86483899|gb|CI126532.1|CI126532
EST:     ACTGGACGGAGGCCTTTGCAAAGAATTCCTCCACCGGCATGGAAGAAAAG                         GTGCAGAAGCTGGTTGAGATGGGCTTCCCTGAAGACATGGTGAGAAGTGTT
genomic: ACTGGACGGAGGCCTTTGCAAAGAATTCCTCCACCGGCATGGAAGAAAAGgtattgttat ... gcaatcacagGTGCAGAAGCTGGTTGAGATGGGCTTCCCTGAAGACATGGTGAGAAGTGTT
EST: gi|88205918|gb|CI205767.1|CI205767
EST:     ACTGGACGGAGGCCTTTGCAAAGAATTCCTCCACCGGCATGGAAGAAAAG                         GTGCAGAAGCTGGTTGAGATGGGCTTCCCTGAAGACATGGTGAGAAGTGTT
genomic: ACTGGACGGAGGCCTTTGCAAAGAATTCCTCCACCGGCATGGAAGAAAAGgtattgttat ... gcaatcacagGTGCAGAAGCTGGTTGAGATGGGCTTCCCTGAAGACATGGTGAGAAGTGTT
EST: gi|86599379|gb|CI251337.1|CI251337
EST:     ACTGGACGGAGGCCTTTGCAAAGAATTCCTCCACCGGCATGGAAGAAAAG                         GTGCAGAAGCTGGTTGAGATGGGCTTCCCTGAAGACATGGTGAGAAGTGTT
genomic: ACTGGACGGAGGCCTTTGCAAAGAATTCCTCCACCGGCATGGAAGAAAAGgtattgttat ... gcaatcacagGTGCAGAAGCTGGTTGAGATGGGCTTCCCTGAAGACATGGTGAGAAGTGTT
EST: gi|86418458|gb|CI032667.1|CI032667
EST:     ACTGGACGGAGGCCTTTGCAAAGAATTCCTCCACCGGCATGGAAGAAAAG                         GTGCAGAAGCTGGTTGAGATGGGCTTCCCTGAAGACATGGTGAGAAGTGTT
genomic: ACTGGACGGAGGCCTTTGCAAAGAATTCCTCCACCGGCATGGAAGAAAAGgtattgttat ... gcaatcacagGTGCAGAAGCTGGTTGAGATGGGCTTCCCTGAAGACATGGTGAGAAGTGTT
EST: gi|88455407|gb|CI519428.1|CI519428
EST:     ACTGGACGGAGGCCTTTGCAAAGAATTCCTCCACCGGCATGGAAGAAAAG                         GTGCAGAAGCTGGTTGAGATGGGCTTCCCTGAAGACATGGTGAGAAGTGTT
genomic: ACTGGACGGAGGCCTTTGCAAAGAATTCCTCCACCGGCATGGAAGAAAAGgtattgttat ... gcaatcacagGTGCAGAAGCTGGTTGAGATGGGCTTCCCTGAAGACATGGTGAGAAGTGTT
EST: gi|86542895|gb|CI183101.1|CI183101
EST:     ACTGGACGGAGGCCTTTGCAAAGAATTCCTCCACCGGCATGGAAGAAAAG                         GTGCAGAAGCTGGTTGAGATGGGCTTCCCTGAAGACATGGTGAGAAGTGTT
genomic: ACTGGACGGAGGCCTTTGCAAAGAATTCCTCCACCGGCATGGAAGAAAAGgtattgttat ... gcaatcacagGTGCAGAAGCTGGTTGAGATGGGCTTCCCTGAAGACATGGTGAGAAGTGTT
EST: gi|86543948|gb|CI184154.1|CI184154
EST:     ACTGGACGGAGGCCTTTGCAAAGAATTCCTCCACCGGCATGGAAGAAAAG                         GTGCAGAAGCTGGTTGAGATGGGCTTCCCTGAAGACATGGTGAGAAGTGTT
genomic: ACTGGACGGAGGCCTTTGCAAAGAATTCCTCCACCGGCATGGAAGAAAAGgtattgttat ... gcaatcacagGTGCAGAAGCTGGTTGAGATGGGCTTCCCTGAAGACATGGTGAGAAGTGTT
EST: gi|86507774|gb|CI150407.1|CI150407
EST:     ACTGGACGGAGGCCTTTGCAAAGAATTCCTCCACCGGCATGGAAGAAAAG                         GTGCAGAAGCTGGTTGAGATGGGCTTCCCTGAAGACATGGTGAGAAGTGTT
genomic: ACTGGACGGAGGCCTTTGCAAAGAATTCCTCCACCGGCATGGAAGAAAAGgtattgttat ... gcaatcacagGTGCAGAAGCTGGTTGAGATGGGCTTCCCTGAAGACATGGTGAGAAGTGTT
EST: gi|3762498|gb|AU029250.1|AU029250
EST:     ACTGGACGGAGGCCTTTGCAAAGAATTCCTCCACCGGNATGGAAGAAAAG                         GTGCAGAAGCTGGTTGAGATGGGCTTCCCTGAAGACATGGTGAGAAGTGTT
genomic: ACTGGACGGAGGCCTTTGCAAAGAATTCCTCCACCGGCATGGAAGAAAAGgtattgttat ... gcaatcacagGTGCAGAAGCTGGTTGAGATGGGCTTCCCTGAAGACATGGTGAGAAGTGTT
EST: gi|88472915|gb|CI410186.1|CI410186
EST:     ACTGGACGGAGGCCTTTGCAAAGAATTCCTCCACCGGCATGGAAGAAAAG                         GTGCAGAAGCTGGTTGAGATGGGCTTCCCTGAAGACATGGTGAGAAGTGTT
genomic: ACTGGACGGAGGCCTTTGCAAAGAATTCCTCCACCGGCATGGAAGAAAAGgtattgttat ... gcaatcacagGTGCAGAAGCTGGTTGAGATGGGCTTCCCTGAAGACATGGTGAGAAGTGTT
EST: gi|88238860|gb|CI236711.1|CI236711
EST:     ACTGGACGGAGGCCTTTGCAAAGAATTCCTCCACCGGCATGGAAGAAAAG                         GTGCAGAAGCTGGTTGAGATGGGCTTCCCTGAAGACATGGTGAGAAGTGTT
genomic: ACTGGACGGAGGCCTTTGCAAAGAATTCCTCCACCGGCATGGAAGAAAAGgtattgttat ... gcaatcacagGTGCAGAAGCTGGTTGAGATGGGCTTCCCTGAAGACATGGTGAGAAGTGTT
EST: gi|88264444|gb|CI368218.1|CI368218
EST:     ACTGGACGGAGGCCTTTGCAAAGAATTCCTCCACCGGCATGGAAGAAAAG                         GTGCAGAAGCTGGTTGAGATGGGCTTCCCTGAAGACATGGTGAGAAGTGTT
genomic: ACTGGACGGAGGCCTTTGCAAAGAATTCCTCCACCGGCATGGAAGAAAAGgtattgttat ... gcaatcacagGTGCAGAAGCTGGTTGAGATGGGCTTCCCTGAAGACATGGTGAGAAGTGTT
EST: gi|3762499|gb|AU029251.1|AU029251
EST:     ACTGGACGGAGGCCTTTGCAAAGAATTCCTCCACCGGCATGGAAGAAAAG                         GTGCAGAAGNTGGTTGAGATGGGCTTCCCTGAAGACATGGTGAGAAGTGTT
genomic: ACTGGACGGAGGCCTTTGCAAAGAATTCCTCCACCGGCATGGAAGAAAAGgtattgttat ... gcaatcacagGTGCAGAAGCTGGTTGAGATGGGCTTCCCTGAAGACATGGTGAGAAGTGTT
EST: gi|88212778|gb|CI212418.1|CI212418
EST:     ACTGGACGGAGGCCTTTGCAAAGAATTCCTCCACCGGCATGGAAGAAAAG                         GTGCAGAAGCTGGTTGAGATGGGCTTCCCTGAAGACATGGTGAGAAGTGTT
genomic: ACTGGACGGAGGCCTTTGCAAAGAATTCCTCCACCGGCATGGAAGAAAAGgtattgttat ... gcaatcacagGTGCAGAAGCTGGTTGAGATGGGCTTCCCTGAAGACATGGTGAGAAGTGTT
EST: gi|3767494|gb|AU031604.1|AU031604
EST:     ACTGGACGGAGGCCTTTGCAAAGAATTCCTCCACCGGCATGGAAGAAAAG                         GTGCAGAAGCTGGTTGAGATGGGCTTCCCTGAAGACATGGTGAGAAGTGTT
genomic: ACTGGACGGAGGCCTTTGCAAAGAATTCCTCCACCGGCATGGAAGAAAAGgtattgttat ... gcaatcacagGTGCAGAAGCTGGTTGAGATGGGCTTCCCTGAAGACATGGTGAGAAGTGTT
EST: gi|86841946|gb|CI338356.1|CI338356
EST:     ACTGGACGGAGGCCTTTGCAAAGAATTCCTCCACCGGCATGGAAGAAAAG                         GTGCAGAAGCTGGTTGAGATGGGCTTCCCTGAAGACATGGTGAGAAGTGGT
genomic: ACTGGACGGAGGCCTTTGCAAAGAATTCCTCCACCGGCATGGAAGAAAAGgtattgttat ... gcaatcacagGTGCAGAAGCTGGTTGAGATGGGCTTCCCTGAAGACATGGTGAGAAGTG-T

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: 49 (upstream exon), 62 (downstream exon)
Score: 20

TACTTGCGTGACTATTCCACATTTTCTGCTACTGCTCGCTACTGGACGGAGGCCTTTGCAAAGAATTCCTCCACCGGCATGGAAGAAAAGgtattgttat ... gcaatcacagGTGCAGAAGCTGGTTGAGATGGGCTTCCCTGAAGACATGGTGAGAAGTGTTCTGAAGAGTGTCAATGGCGACGAGAACATGGCTCTTGAGAAGCTCTGCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgggtatacagaagttgtagataccgtagtaaaatactccattctgcaatcacagGTGCAGAAGCTGGTTGAGATGGGCTTCCCTGAAGACATGGTGAGAAGTGTTCTGAAGAGTGTCAATGGCGACGAGAACATGGCTCTTGAGAAGCTCTGCT
                          tagtaaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgttattgaggagtactcatatttattgttccagtgggtatacagaagttgtagataccgtagtaaaatactccattctgcaatcacagGTGCAGAAGCTGGTTGAGATGGGCTTCCCTGAAGACATGGTGAGAAGTGTTCTGAAGAGTGTCAATGGCGACGAGAACATGGCTCTTGAGAAGCTCTGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC