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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACAAGCTAAAAGGGACAATTAAAGTGGCTGCAATCAAGGCCCCTTCCTTTGGGGAACAAATGACTCAATGTTTGGATGACATTGCCATCATGACAGGAGgtataataccttacagaggttactaaaaagacttttaaatagatgaatgcaaccacatcatcaacatattttcattgcttttcag

Basic information

species Oryza sativa
transcript 13113.m00214
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: 13113.m00214 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G042253_T01 (Zea mays), 5'ss of exon 5
AACAAGCTAAAAGGGACAATTAAAGTGGCTGCAATCAAGGCCCCTTCCTTTGGGGAACAAATGACTCAATGTTTGGATGACATTGCCATCATGACAGGAGgtataataccttacagaggttactaaaaagacttttaaatagatgaatgcaaccaca-tcatcaacatattttcattgcttttcag
|||||||| |||||||||||||| || || ||  | ||||||   || ||||||||||||| ||||||||| |||||||||||||| |||||||||||||||| |  ||   |||                     ||    |  |||||||  ||| ||  |||| |||| || ||| |||||||
AACAAGCTGAAAGGGACAATTAAGGTTGCAGCCGTTAAGGCCTTCTCTTTTGGGGAACAAAAGACTCAATGCTTGGATGACATTGCAATCATGACAGGAGgtacagaactcgaca-------------------ccaacctaaccaatgcaattacagtctccaacgtattctcgttggttttcag
















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|58689939|gb|CK078626.1|CK078626
EST:     TGGGGAACAAATGACTCAATGTTTGGATGACATTGCCATCATGACAGGAG                         GTACACTAGTGCGTGAAGACATGGGATATACACTAGAAAAGGCAGGGAAAG
genomic: TGGGGAACAAATGACTCAATGTTTGGATGACATTGCCATCATGACAGGAGgtataatacc ... tgcttttcagGTACACTAGTGCGTGAAGACATGGGATATACACTAGAAAAGGCAGGGAAAG
EST: gi|29668864|gb|CB665139.1|CB665139
EST:     TGGGGAACAAATGACTCAATGTTTGGATGACATTGCCATCATGACAGGAG                         GTACACTAGTGCGTGAAGACATGGGATATACACTAGAAAAGGCACGGAAAG
genomic: TGGGGAACAAATGACTCAATGTTTGGATGACATTGCCATCATGACAGGAGgtataatacc ... tgcttttcagGTACACTAGTGCGTGAAGACATGGGATATACACTAGAAAAGGCAGGGAAAG
EST: gi|58688418|gb|CK077105.1|CK077105
EST:     TGGGGAACAAATGACTCAATGTTTGGATGACATTGCCATCATGACAGGAG                         GTACACTAGTGCGTGAAGACATGGGATATACACTAGAAAAGGCAGGGAAAG
genomic: TGGGGAACAAATGACTCAATGTTTGGATGACATTGCCATCATGACAGGAGgtataatacc ... tgcttttcagGTACACTAGTGCGTGAAGACATGGGATATACACTAGAAAAGGCAGGGAAAG
EST: gi|58692944|gb|CK081631.1|CK081631
EST:     TGGGGAACAAATGACTCAATGTTTGGATGACATTGCCATCATGACAGGAG                         GTACACTAGTGCGTGAAGACATGGGATATACACTAGAAAAGGCAGGGAAAG
genomic: TGGGGAACAAATGACTCAATGTTTGGATGACATTGCCATCATGACAGGAGgtataatacc ... tgcttttcagGTACACTAGTGCGTGAAGACATGGGATATACACTAGAAAAGGCAGGGAAAG
EST: gi|29638632|gb|CB643641.1|CB643641
EST:     TGGGGAACAAATGACTCAATGTTTGGATGACATTGCCATCATGACAGGAG                         GTACACTAGTGCGTGAAGACATGGGATATACACTAGAAAAGGCAGGGAAAG
genomic: TGGGGAACAAATGACTCAATGTTTGGATGACATTGCCATCATGACAGGAGgtataatacc ... tgcttttcagGTACACTAGTGCGTGAAGACATGGGATATACACTAGAAAAGGCAGGGAAAG
EST: gi|58612906|gb|CK040618.1|CK040618
EST:     TGGGGAACAAATGACTCAATGTTTGGATGACATTGCCATCATGACAGGAG                         GTACACTAGTGCGTGAAGACATGGGATATACACTAGAAAAGGCAGGGAAAG
genomic: TGGGGAACAAATGACTCAATGTTTGGATGACATTGCCATCATGACAGGAGgtataatacc ... tgcttttcagGTACACTAGTGCGTGAAGACATGGGATATACACTAGAAAAGGCAGGGAAAG
EST: gi|29668896|gb|CB665171.1|CB665171
EST:     TGGGGAACAAATGACTCAATGTTTGGATGACATTGCCATCATGACAGGAG                         GTACACTAGTGCGTGAAGACATGGGATATACACTAGAAAAGGCAGGGAAAG
genomic: TGGGGAACAAATGACTCAATGTTTGGATGACATTGCCATCATGACAGGAGgtataatacc ... tgcttttcagGTACACTAGTGCGTGAAGACATGGGATATACACTAGAAAAGGCAGGGAAAG
EST: gi|58691639|gb|CK080326.1|CK080326
EST:     TGGGGAACAAATGACTCAATGTTTGGATGACATTGCCATCATGACAGGAG                         GTACACTAGTGCGTGCAAGACATGGGATATACACTAGAAAAGGCAGGGAAA
genomic: TGGGGAACAAATGACTCAATGTTTGGATGACATTGCCATCATGACAGGAGgtataatacc ... tgcttttcagGTACACTAGTGCGTG-AAGACATGGGATATACACTAGAAAAGGCAGGGAAA

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: 72 (upstream exon), 50 (downstream exon)
Score: 8

AACAAGCTAAAAGGGACAATTAAAGTGGCTGCAATCAAGGCCCCTTCCTTTGGGGAACAAATGACTCAATGTTTGGATGACATTGCCATCATGACAGGAGgtataatacc ... tgcttttcagGTACACTAGTGCGTGAAGACATGGGATATACACTAGAAAAGGCAGGGAAAGAGGTTCTAGGTTCTGCTTCTAAGGTTGTAGTCGGGAAAGACTCAACACT




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