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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaaatgtgtaactttcatgaaaaccaaggtatataaaaatcttcatttcacatatagaattttctttctttcatttcattgcagGGCTTTCTTGTTGGTTCTTATGGGCTGACGTGGGCACTCAATAACTCAAGCAAAGTCCTTAAATTAGCAATCCTTAACAGTCCTCTTACAGTTTCTTCTC

Basic information

species Zea mays
transcript GRMZM2G117531_T04
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G117531_T04 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os04g55180.1 (Oryza sativa), 3'ss of exon 5
gtacaaatgtgtaactttcatgaaaaccaaggtatataaaaatcttcatttcacatatagaattttctttctttcattt-cattgcagGGCTTTCTTGTTGGTTCTTATGGGCTGACGTGGGCACTCAATAACTCAAGCAAAGTCCTTAAATTAGCAATCCTTAACAGTCCTCTTACAGTTTCTTCTC
|||||       ||| || | |||     |  |  |||| |||  |||| | | || |      |  |||||||||||| ||||  |||| |||||||| ||||| |||||||| || |||||||| || |||||||||||||| || ||  ||||||| ||||||||||| || || ||||||||||
gtacatgcccaaaacatt-aggaacctgcattttcataataattctcatat-atattttctgaatcgtttctttcattttcattctagGGATTTCTTGTAGGTTCATATGGGCTAACATGGGCACTAAAGAACTCAAGCAAAGTTCTGAAGGTAGCAATTCTTAACAGTCCACTCACTGTTTCTTCTC
















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|5325076|gb|AI783267.1|AI783267
EST:     ATCTTCTTGGTACTCTAAATATCACCGAGCCCTTCTTCTTAGTTGTCCAG                         GGCTTTCTTGTTGGTTCTTATGGGCTGACGTGGGCACTGAATAACTCAAGC
genomic: ATCTTCTTGGTACTCTAAATATCACCGAGCCCTTCTTCTTAGTTGTCCAGgtacaaatgt ... ttcattgcagGGCTTTCTTGTTGGTTCTTATGGGCTGACGTGGGCACTCAATAACTCAAGC
EST: gi|5846888|gb|AI999971.1|AI999971
EST:     ATCTTCTTGGTACTCTAAATATCACCGAGCCCTTCTTCTTAGTTGTCCAG                         GGCTTTCTTGTTGGTTCTTATGGGCTGACGTGGGCACTGAATAACTCAAGC
genomic: ATCTTCTTGGTACTCTAAATATCACCGAGCCCTTCTTCTTAGTTGTCCAGgtacaaatgt ... ttcattgcagGGCTTTCTTGTTGGTTCTTATGGGCTGACGTGGGCACTCAATAACTCAAGC
EST: gi|149001509|gb|EE038815.2|EE038815
EST:     ATCTTCTTGGTACTCTAAATATCACCGAGCCCTTCTTCTTAGTTGTCCAG                         GGCTTTCTTGTTGGTTCTTA
genomic: ATCTTCTTGGTACTCTAAATATCACCGAGCCCTTCTTCTTAGTTGTCCAGgtacaaatgt ... ttcattgcagGGCTTTCTTGTTGGTTCTTA
EST: gi|148964993|gb|EC906065.2|EC906065
EST:     ATCTTCTTGGTACTCTAAATATCACCGAGCCCTTCTTCTGAGTTGTCCAG                         GGCTTTCTCGTTGGTTCTTATGGGCTGACGTGGGCACTCAATAACTCAAGA
genomic: ATCTTCTTGGTACTCTAAATATCACCGAGCCCTTCTTCTTAGTTGTCCAGgtacaaatgt ... ttcattgcagGGCTTTCTTGTTGGTTCTTATGGGCTGACGTGGGCACTCAATAACTCAAGC
EST: gi|148947866|gb|EC893357.2|EC893357
EST:     ATCTTCTTGGTACTCTAAATATCACCGAGCCCTTCTTCCTAGTTGTCCAG                         GGCTTTTCT-GTTGGTTCTT
genomic: ATCTTCTTGGTACTCTAAATATCACCGAGCCCTTCTTCTTAGTTGTCCAGgtacaaatgt ... ttcattgcagGGCTTT-CTTGTTGGTTCTT

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 4 RNA-Seq libraries.


Block sizes: 36 (upstream exon), 44 (downstream exon)
Score: 11

AGGACGAATTTCACAAGGCATTTGATGATCTTCTTGGTACTCTAAATATCACCGAGCCCTTCTTCTTAGTTGTCCAGgtacaaatgt ... ttcattgcagGGCTTTCTTGTTGGTTCTTATGGGCTGACGTGGGCACTCAATAACTCAAGCAAAGTCCTTAAATTAGCAATCCTTAACAGTCCTCTTACAGTTTCTTCTC


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 36

AGGACGAATTTCACAAGGCATTTGATGATCTTCTTGGTACTCTAAATATCACCGAGCCCTTCTTCTTAGTTGTCCAGgtacaaatgt ... ttcattgcagGGCTTTCTTGTTGGTTCTTATGGGCTGACGTGGGCACTCAATAACTCAAGCAAAGTCCTTAAATTAGCAATCCTTAACAGTCCTCTTACAGTTTCTTCTC


Block sizes: 47 (upstream exon), 26 (downstream exon)
Score: 3

AGGACGAATTTCACAAGGCATTTGATGATCTTCTTGGTACTCTAAATATCACCGAGCCCTTCTTCTTAGTTGTCCAGgtacaaatgt ... ttcattgcagGGCTTTCTTGTTGGTTCTTATGGGCTGACGTGGGCACTCAATAACTCAAGCAAAGTCCTTAAATTAGCAATCCTTAACAGTCCTCTTACAGTTTCTTCTC


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 15

AGGACGAATTTCACAAGGCATTTGATGATCTTCTTGGTACTCTAAATATCACCGAGCCCTTCTTCTTAGTTGTCCAGgtacaaatgt ... ttcattgcagGGCTTTCTTGTTGGTTCTTATGGGCTGACGTGGGCACTCAATAACTCAAGCAAAGTCCTTAAATTAGCAATCCTTAACAGTCCTCTTACAGTTTCTTCTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatataaaaatcttcatttcacatatagaattttctttctttcatttcattgcagGGCTTTCTTGTTGGTTCTTATGGGCTGACGTGGGCACTCAATAACTCAAGCAAAGTCCTTAAATTAGCAATCCTTAACAGTCCTCTTACAGTTTCTTCTC
                              ttttctttctttcatt  CT-rich tract
                      atatagaattttcttt  TA-rich tract