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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaagtgtttttccatctatacaattagcgacagttgttaacaactattcatttattatagctaattattttttgacagGTTGCTGACTCCTACTGAAACTATGTGAAGGCCGTTTTCCTCCACTTGTATAATCATTGGGCGTGCTTTAAGATCGGCATATCCGACGATAAAACCCACA

Basic information

species Oryza sativa
transcript LOC_Os02g11830.2
intron # 25
splice site 3'
intron type U2

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|88436253|gb|CI519172.1|CI519172
EST:     TAGTGAATCAGCGGGACAGCAACCTGATACACTGATTCAGGCTTGTGAAG                         GTTGCTGACTCCTACTGAAACTATGTGAAGGCCGTTTTCCTCCACTTGTAT
genomic: TAGTGAATCAGCGGGACAGCAACCTGATACACTGATTCA-GCTTGTAAAGgtgaagtgtt ... tttttgacagGTTGCTGACTCCTACTGAAACTATGTGAAGGCCGTTTTCCTCCACTTGTAT
EST: gi|88281294|gb|CI402690.1|CI402690
EST:     ATAGTGAATCAGCGGGACAGCAACCTGATACACTGATTCAGCTTGTAAAG                         GTTGCTGACTCCTACTGAAACTATGTGAAGGCCGTTTTCCTCCACTTGTAT
genomic: ATAGTGAATCAGCGGGACAGCAACCTGATACACTGATTCAGCTTGTAAAGgtgaagtgtt ... tttttgacagGTTGCTGACTCCTACTGAAACTATGTGAAGGCCGTTTTCCTCCACTTGTAT
EST: gi|88321171|gb|CI532921.1|CI532921
EST:     ATAG-GAATCAGGGGGACAGCAACCTGATACACTGATTCAGGTTGTAAAG                         GTTGCTGACTCCTAGTGAAACTATGTGAAGGCCGTTTTCCTCCACTTGTAT
genomic: ATAGTGAATCAGCGGGACAGCAACCTGATACACTGATTCAGCTTGTAAAGgtgaagtgtt ... tttttgacagGTTGCTGACTCCTACTGAAACTATGTGAAGGCCGTTTTCCTCCACTTGTAT
EST: gi|86430195|gb|CI082618.1|CI082618
EST:     ATAGTGAATCAGCGGGACAGCAACCTGATACACTGATTCAGCTTGTAAAG                         GTTGCTGACTCCTACTGAAACTATGTGAAGGCCGTTTTCCTCCACTTGTAT
genomic: ATAGTGAATCAGCGGGACAGCAACCTGATACACTGATTCAGCTTGTAAAGgtgaagtgtt ... tttttgacagGTTGCTGACTCCTACTGAAACTATGTGAAGGCCGTTTTCCTCCACTTGTAT
EST: gi|27576683|gb|CA999377.1|CA999377
EST:     ATAGTGAATCAGCGGGACAGCAACCTGATACACTGATTCAGCTTGTAAAG                         GTTGCTGACTCCTACTGAAACTATGTG
genomic: ATAGTGAATCAGCGGGACAGCAACCTGATACACTGATTCAGCTTGTAAAGgtgaagtgtt ... tttttgacagGTTGCTGACTCCTACTGAAACTATGTG
EST: gi|86479335|gb|CI121968.1|CI121968
EST:     ATAGTGAATCAGCGGGACAGCAACCTGATACACTGATTCAGCTTGTAAAG                         GTTGCTGACTCCTACTGAAACTATGTGAAGGCCGTTTTCCTCCACTTGTAT
genomic: ATAGTGAATCAGCGGGACAGCAACCTGATACACTGATTCAGCTTGTAAAGgtgaagtgtt ... tttttgacagGTTGCTGACTCCTACTGAAACTATGTGAAGGCCGTTTTCCTCCACTTGTAT
EST: gi|88471322|gb|CI408593.1|CI408593
EST:     ATAGTGAATCAGCGGGACAGCAACCTGATACACTGATTCAGCTTGTAAAG                         GTTGCTGACTCCTACTGAAACTATGTGAAGGCCGTTTTCCTCCACTTGTAT
genomic: ATAGTGAATCAGCGGGACAGCAACCTGATACACTGATTCAGCTTGTAAAGgtgaagtgtt ... tttttgacagGTTGCTGACTCCTACTGAAACTATGTGAAGGCCGTTTTCCTCCACTTGTAT
EST: gi|88828940|gb|CI073810.1|CI073810
EST:     ATAGTGAATCAGCGGGACAGCAACCTGATACACTGATTCAGCTTGTAAAG                         GTTGCTGACTCCTACTGAAACTATGTGAAGGCCGTTTTCCTCCACTTGTAT
genomic: ATAGTGAATCAGCGGGACAGCAACCTGATACACTGATTCAGCTTGTAAAGgtgaagtgtt ... tttttgacagGTTGCTGACTCCTACTGAAACTATGTGAAGGCCGTTTTCCTCCACTTGTAT
EST: gi|88519824|gb|CI447478.1|CI447478
EST:     ATAGTGAATCAGCGGGACAGCAACCTGATACACTGATTCAGCTTGTAAAG                         GTTGCTGACTCCTACTGAAACTATGTGAAGGCCGTTTTCCTCCACTTGTAT
genomic: ATAGTGAATCAGCGGGACAGCAACCTGATACACTGATTCAGCTTGTAAAGgtgaagtgtt ... tttttgacagGTTGCTGACTCCTACTGAAACTATGTGAAGGCCGTTTTCCTCCACTTGTAT
EST: gi|89187347|gb|CI047414.1|CI047414
EST:     ATAGTGAATCAGCGGGACAGCAACCTGATACACTGATTCAGCTTGTAAAG                         GTTGCTGACTCCTACTGAAACTATGTGAAGGCCGTTTTCCTCCACTTGTAT
genomic: ATAGTGAATCAGCGGGACAGCAACCTGATACACTGATTCAGCTTGTAAAGgtgaagtgtt ... tttttgacagGTTGCTGACTCCTACTGAAACTATGTGAAGGCCGTTTTCCTCCACTTGTAT

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: 21 (upstream exon), 42 (downstream exon)
Score: 6

TATTGACTCCTGACCAATAGTGAATCAGCGGGACAGCAACCTGATACACTGATTCAGCTTGTAAAGgtgaagtgtt ... tttttgacagGTTGCTGACTCCTACTGAAACTATGTGAAGGCCGTTTTCCTCCACTTGTATAATCATTGGGCGTGCTTTAAGATCGGCATATCCGACGATAAAACCCACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagcgacagttgttaacaactattcatttattatagctaattattttttgacagGTTGCTGACTCCTACTGAAACTATGTGAAGGCCGTTTTCCTCCACTTGTATAATCATTGGGCGTGCTTTAAGATCGGCATATCCGACGATAAAACCCACA
                                         ttatttttt  CT-rich tract
             ttaacaactattcatt  TA-rich tract