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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttgttattacatggtatactgtgggagcttggtgtgtaacacatttgtatgtctttaacttaactgcttccatggccattcattgttccttatacagGTCACTGCTCTCGATGAGCGGTACAAGCTATCAGAAAGCTGTGACTACGAGGTCAAAGTCGCGTTTCTCCAGCTTGCAATTCCCACCGGCTGCAGATGCT

Basic information

species Oryza sativa
transcript LOC_Os03g60460.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g60460.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G155580_T01 (Zea mays), 3'ss of exon 3
-------tttttgttattacatg-gtatactgtgggagcttggtgtgtaacacatttgtatgtctttaacttaactgcttccatggccattcattgttccttatacagGTCACTGCTCTCGATGAGCGGTACAAGCTATCAGAAAGCTGTGACTACGAGGTCAAAGTCGCGTTTCTCCAGCTTGCAATTCCCACCGGCTGCAGATGCT
       | | | |   || ||   || |       | ||   || || |    |||  |  ||       | ||  | | |||| | ||   || |||   || ||||||||||||||||| ||||||||||||||||| |||||| ||||||||||||||||||| ||||| |||||||| || || |||||||| ||||  ||||
taatatatatatatatatatatatatacatcacaataactcaatgagtga----tttaaagatc----gactgaccacatgcatgcctatatcttcttctgcatgcagGTCACTGCTCTCGACGAGCGGTACAAGCTATCTGAAAGCCGTGACTACGAGGTCAAAGTGGCGTTCCTCCAGCTGGCGATCCCCACCGGGTGCAAGTGCT
















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|89184847|gb|CI048403.1|CI048403
EST:     AATGGGAACTTTACTTGGAAAACTTACCCACAGATGTTGAAGCTTCACAG                         GTCACTGCTCTCGATGAGCGGTACAAGCTATCAGAAAGCTGTGACTACGAG
genomic: AATGGGAACTTTACTTGGAAAACTTACCCACAGATGTTGAAGCTTCACAGgtatgaattc ... ccttatacagGTCACTGCTCTCGATGAGCGGTACAAGCTATCAGAAAGCTGTGACTACGAG
EST: gi|29638327|gb|CB643336.1|CB643336
EST:     AATGGGAACTTTACTTGGAAAACTTACCCACAGATGTTGAAGCTTCACAG                         GTCACTGCTCTCGATGAGCGGTACAAGCTATCAGAAAGCTGTGACTACGAG
genomic: AATGGGAACTTTACTTGGAAAACTTACCCACAGATGTTGAAGCTTCACAGgtatgaattc ... ccttatacagGTCACTGCTCTCGATGAGCGGTACAAGCTATCAGAAAGCTGTGACTACGAG
EST: gi|88202495|gb|CI200850.1|CI200850
EST:     AATGGGAACTTTACTTGGAAAACTTACCCACAGATGTTGAAGCTTCACAG                         GTCACTGCTCTCGATGAGCGGTACAAGCTATCAGAAAGCTGTGACTACGAG
genomic: AATGGGAACTTTACTTGGAAAACTTACCCACAGATGTTGAAGCTTCACAGgtatgaattc ... ccttatacagGTCACTGCTCTCGATGAGCGGTACAAGCTATCAGAAAGCTGTGACTACGAG
EST: gi|86426510|gb|CI071607.1|CI071607
EST:     CACAGATGTTGAAGCTTCACAG                         GTCACTGCTCTCGATGAGCGGTACAAGCTATCAGAAAGCTGTGACTACGAG
genomic: CACAGATGTTGAAGCTTCACAGgtatgaattc ... ccttatacagGTCACTGCTCTCGATGAGCGGTACAAGCTATCAGAAAGCTGTGACTACGAG
EST: gi|29656551|gb|CB652826.1|CB652826
EST:     AATGGGAACTTTACTTGGAAAACTTACCCACAGATGTTGAAGCTTCACAG                         GTCACTGCTCTCGATGAGCGGTACAAGCTATCAGAAAGCTGTGACTACGAG
genomic: AATGGGAACTTTACTTGGAAAACTTACCCACAGATGTTGAAGCTTCACAGgtatgaattc ... ccttatacagGTCACTGCTCTCGATGAGCGGTACAAGCTATCAGAAAGCTGTGACTACGAG
EST: gi|86431621|gb|CI085232.1|CI085232
EST:     CACAGATGTTGAAGCTTCACAG                         GTCACTGCTCTCGATGAGCGGTACAAGCTATCAGAAAGCTGTGACTACGAG
genomic: CACAGATGTTGAAGCTTCACAGgtatgaattc ... ccttatacagGTCACTGCTCTCGATGAGCGGTACAAGCTATCAGAAAGCTGTGACTACGAG
EST: gi|87011453|gb|CI279362.1|CI279362
EST:     AATGGGAACTTTACTTGGAAAACTTACCCACAGATGTTGAAGCTTCACAG                         GTCACTGCTCTCGATGAGCGGTACAAGCTATCAGAAAGCTGTGACTACGAG
genomic: AATGGGAACTTTACTTGGAAAACTTACCCACAGATGTTGAAGCTTCACAGgtatgaattc ... ccttatacagGTCACTGCTCTCGATGAGCGGTACAAGCTATCAGAAAGCTGTGACTACGAG
EST: gi|86433038|gb|CI093381.1|CI093381
EST:     CCACAGATGTTGAAGCTTCACAG                         GTCACTGCTCTCGATGAGCGGTACAAGCTATCAGAAAGCTGTGACTACGAG
genomic: CCACAGATGTTGAAGCTTCACAGgtatgaattc ... ccttatacagGTCACTGCTCTCGATGAGCGGTACAAGCTATCAGAAAGCTGTGACTACGAG
EST: gi|88956048|gb|CI092336.1|CI092336
EST:     AAGCTTCACAG                         GTCACTGCTCTCGATGAGCGGTACAAGCTATCAGAAAGCTGTGACTACGAG
genomic: AAGCTTCACAGgtatgaattc ... ccttatacagGTCACTGCTCTCGATGAGCGGTACAAGCTATCAGAAAGCTGTGACTACGAG
EST: gi|86500389|gb|CI143022.1|CI143022
EST:     AATGGGAACTTTACTTGGAAAACTTACCCACAGATGTTGAAGCTTCACAG                         GTCACTGCTCTCGATGAGCGGTACAAGCTATCAGAAAGCTGTGACTACGAG
genomic: AATGGGAACTTTACTTGGAAAACTTACCCACAGATGTTGAAGCTTCACAGgtatgaattc ... ccttatacagGTCACTGCTCTCGATGAGCGGTACAAGCTATCAGAAAGCTGTGACTACGAG
EST: gi|89183464|gb|CI046029.1|CI046029
EST:     AATGGGAACTTTACGTGGAAAACTTACCCACAGATGTTGAAGCTTCACAG                         GTCACTGCTCTCGATGAGCGGTACAAGCTATCAGAAAGCTGTGACTACGAG
genomic: AATGGGAACTTTACTTGGAAAACTTACCCACAGATGTTGAAGCTTCACAGgtatgaattc ... ccttatacagGTCACTGCTCTCGATGAGCGGTACAAGCTATCAGAAAGCTGTGACTACGAG
EST: gi|89192696|gb|CI049994.1|CI049994
EST:     ATGTTGAAGCTTCACAG                         GTCACTGCTCTCGATGAGCGGTACAAGCTATCAGAAAGCTGTGACTACGAG
genomic: ATGTTGAAGCTTCACAGgtatgaattc ... ccttatacagGTCACTGCTCTCGATGAGCGGTACAAGCTATCAGAAAGCTGTGACTACGAG
EST: gi|33683161|gb|CF311400.1|CF311400
EST:     AATGGGAACTTTACTTGGAAAACTTACCCACAGATGTTGAAGCTTCACAG                         GTCACTGCTCTCGATGAGCGGTACAAGCTATCAGAAAGCTGTGACTACGAG
genomic: AATGGGAACTTTACTTGGAAAACTTACCCACAGATGTTGAAGCTTCACAGgtatgaattc ... ccttatacagGTCACTGCTCTCGATGAGCGGTACAAGCTATCAGAAAGCTGTGACTACGAG
EST: gi|88848002|gb|CI086524.1|CI086524
EST:     CCCACAGATGTTGAAGCTTCACAG                         GTCACTGCTCTCGATGAGCGGTACAAGCTATCAGAAAGCTGTGACTACGAG
genomic: CCCACAGATGTTGAAGCTTCACAGgtatgaattc ... ccttatacagGTCACTGCTCTCGATGAGCGGTACAAGCTATCAGAAAGCTGTGACTACGAG
EST: gi|89169533|gb|CI109892.1|CI109892
EST:     GAAGCTTCACAG                         GTCACTGCTCTCGATGAGCGGTACAAGCTATCAGAAAGCTGTGACTACGAG
genomic: GAAGCTTCACAGgtatgaattc ... ccttatacagGTCACTGCTCTCGATGAGCGGTACAAGCTATCAGAAAGCTGTGACTACGAG
EST: gi|89186047|gb|CI047916.1|CI047916
EST:     CACAGATGTTGAAGCTTCACAG                         GTCACTGCTCTCGATGAGCGGTACAAGCTATCAGAAAGCTGTGACTACGAG
genomic: CACAGATGTTGAAGCTTCACAGgtatgaattc ... ccttatacagGTCACTGCTCTCGATGAGCGGTACAAGCTATCAGAAAGCTGTGACTACGAG
EST: gi|86434643|gb|CI105876.1|CI105876
EST:     AATGGGAACTTTACTTGGAAAACTTACCCACAGATGTTGAAGCTTCACAG                         GTCACTGCTCTCGATGAGCGGTACAAGCTATCAGAAAGCTGTGACTACGAG
genomic: AATGGGAACTTTACTTGGAAAACTTACCCACAGATGTTGAAGCTTCACAGgtatgaattc ... ccttatacagGTCACTGCTCTCGATGAGCGGTACAAGCTATCAGAAAGCTGTGACTACGAG
EST: gi|33683162|gb|CF311401.1|CF311401
EST:     TGGGAACTTTACTTGGAAAACTTANNNNNNNAGATGTTGAAGCTTCACAG                         GTCACTGCTCTCGATGAGCGGTACAAGCTATCAGAAAGCTGTGACTACGAG
genomic: TGGGAACTTTACTTGGAAAACTTA--CCCACAGATGTTGAAGCTTCACAGgtatgaattc ... ccttatacagGTCACTGCTCTCGATGAGCGGTACAAGCTATCAGAAAGCTGTGACTACGAG
EST: gi|58604239|gb|CK014767.1|CK014767
EST:     AATGGGAACTTTACTTGGAAAACTTACCCACAGATGTTGAAGCTTCACAG                         GTCACTGCTCTCGATGAGCGGTACAAGCTATCAGAAAGCCGTGACTACGAG
genomic: AATGGGAACTTTACTTGGAAAACTTACCCACAGATGTTGAAGCTTCACAGgtatgaattc ... ccttatacagGTCACTGCTCTCGATGAGCGGTACAAGCTATCAGAAAGCTGTGACTACGAG
EST: gi|87037708|gb|CI192330.1|CI192330
EST:     AATGGGAACTTTACTTGGAAAACTTACCCACAGATGTTGAAGCTTCACAG                         GTCACTGCTCTCGATGAGCGGTACAAGCTATCAGAAAGCTGCGACTACGAG
genomic: AATGGGAACTTTACTTGGAAAACTTACCCACAGATGTTGAAGCTTCACAGgtatgaattc ... ccttatacagGTCACTGCTCTCGATGAGCGGTACAAGCTATCAGAAAGCTGTGACTACGAG

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), 71 (downstream exon)
Score: 17

GTCTGGAAAACTTCCAAGTGAAGATGAGGTAGCAGACTGGAGTGGACAGGAATGGGAACTTTACTTGGAAAACTTACCCACAGATGTTGAAGCTTCACAGgtatgaattc ... ccttatacagGTCACTGCTCTCGATGAGCGGTACAAGCTATCAGAAAGCTGTGACTACGAGGTCAAAGTCGCGTTTCTCCAGCTTGCAATTCCCACCGGCTGCAGATGCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttgtatgtctttaacttaactgcttccatggccattcattgttccttatacagGTCACTGCTCTCGATGAGCGGTACAAGCTATCAGAAAGCTGTGACTACGAGGTCAAAGTCGCGTTTCTCCAGCTTGCAATTCCCACCGGCTGCAGATGCT
               acttaac  putative branch site (score: 17)
                                        ttgttcctt  putative PPT
           tttaacttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttgttattacatggtatactgtgggagcttggtgtgtaacacatttgtatgtctttaacttaactgcttccatggccattcattgttccttatacagGTCACTGCTCTCGATGAGCGGTACAAGCTATCAGAAAGCTGTGACTACGAGGTCAAAGTCGCGTTTCTCCAGCTTGCAATTCCCACCGGCTGCAGATGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - -ttacatg
- - - - - - - - - - - - - - - cttggtg
- - - - - - - - - - - - - - - - - - - - - - - -ttgtatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gccattc