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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGGCCCTGCAATTGCTGGCTACGAGACGgtattatcactggttctgttaattaactacatgacaaaattgttgtgtttacttcctactgatttgcactttttgttgttctgtag

Basic information

species Zea mays
transcript GRMZM2G044011_T02
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044011_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os04g56480.1 (Oryza sativa), 5'ss of exon 7
CATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGGCCCTGCAATTGCTGGCTACGAGACGgtattatcactggttctgttaattaactacatgacaaaattgttgtgtttacttcctactgatttgcactttttgttgttctgtag
|||||||| |||| | ||||||||||||||||| |||||| |||||||||||||||| |||||||| || ||| ||||||    |||||||||| ||      |   | |   ||||||| | | || | || ||||| ||     ||||| | || |||||
CATAACAGTAACCAGAGCACGTATTGAAACATCTATTCCTCGGAAGCATGGCCCTGCGATTGCTGGTTATGAGTCGgtatggaaactggttctgata-----ttgtgtaatctaattgttctatctattcccaactgactt---tgttttgctcttttgtag

upper sequence: GRMZM2G044011_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA10G31310.1 (Glycine max), 5'ss of exon 8
CATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGGCCCTGCAATTGCTGGCTACGAGACGgtattatcactggttctgttaattaactacatgacaaaattgttgtgtttacttcctactgattt---gcactttttgttgttctgtag
 || || |  || ||  | || || ||||||||||||||| | || ||||| |||||||||||||| || ||||  |||| ||| ||   | |  |||   |       |  || |   |   |||   |   ||  || |   |||   |      || |||||
TATGACTGTTACTCGTTCGCGGATAGAAACATCAATTCCTCGCAAACATGGGCCTGCAATTGCTGGTTATGAGAAAgtatgatctctctctattgtaagatatcggtgaatgaattcaata-atttgagtgacacaaatctaaagcatcctcctcctttttgtag

upper sequence: GRMZM2G044011_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA20G36200.1 (Glycine max), 5'ss of exon 8
CATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGGCCCTGCAATTGCTGGCTACGAGACGgtattatcactggttctgttaattaactaca-tgacaaaattgttgtgtttacttcctactgattt---gcactttttgttgttctgtag
 || || |  || ||  | || || ||||||||||||||| | || ||||| |||||||||||||| || ||||  |||| ||| ||   ||| ||     |   || |||   ||||      |||   |  |||  || |   |||   |      || |||||
TATGACTGTTACTCGTTCGCGGATAGAAACATCAATTCCTCGCAAACATGGGCCTGCAATTGCTGGTTATGAGAAAgtatgatctctctctctattgtaagatatcagtgaatgaattcaataatttgaatgatacgaatctaaggcatcctcctcccttttgtag

upper sequence: GRMZM2G044011_T01 (Zea mays), 5'ss of exon 8
lower sequence: AT4G27650.1 (Arabidopsis thaliana), 5'ss of exon 9
CATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGGCCCTGCAATTGCTGGCTACGAGACGgtattatcactggttctgttaattaactacatgac-aaaattgttgtgtttactt--cctactgatttg---cactttttgttgttctgtag
  | |||   | ||| ||||| || |||||||| ||||||||||||||||| |||||||||||||| |||||| | ||||  ||  |   | | ||  | |  ||  || | ||||||  | |   || ||  |||    ||||    || |||||| |  |||||||
TGTGACAAGTAGCCGTGCACGAATAGAAACATCCATTCCTAGGAAGCATGGACCTGCAATTGCTGGTTACGAGTCTgtatgttccttcactgt-ttcgtcatatatgtgcccaaaattcgtttacatatttatcctttcaatttatgtcattttttgcttctctgtag

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|67018605|gb|CO447354.1|CO447354
EST:     GCCCTGCAATTGCTGGCTACGAGACG                         GCCCTCAAGAAGTTCTTTGAGTATGTTTTGCAA
genomic: GCCCTGCAATTGCTGGCTACGAGACGgtattatcac ... tgttctgtagGCCCTCAAGAAGTTCTTTGAGTATGTTTTGCAA
EST: gi|67024357|gb|CO453106.1|CO453106
EST:     AAACATCAATTCCTAGGAAGCATGGCCCTGCAATTGCTGGCTACGAGACG                         GCCCTCAAGAAGTTCTTTGAGTATGTTTTGCAA
genomic: AAACATCAATTCCTAGGAAGCATGGCCCTGCAATTGCTGGCTACGAGACGgtattatcac ... tgttctgtagGCCCTCAAGAAGTTCTTTGAGTATGTTTTGCAA
EST: gi|71763506|gb|DR961443.1|DR961443
EST:     AAACATCAATCCCTAGGAAGCATGGCCCTGCAATTGCTGGCTACGAGACG                         GCCCTCAAGAAGTTCTTTGAGTATGTTTTGCAA
genomic: AAACATCAATTCCTAGGAAGCATGGCCCTGCAATTGCTGGCTACGAGACGgtattatcac ... tgttctgtagGCCCTCAAGAAGTTCTTTGAGTATGTTTTGCAA
EST: gi|71442136|gb|DR823186.1|DR823186
EST:     AAACATCAATTCCTAGAAAGCATGGCCCTGCAATTGCTGACTACGAGACG                         GCCCTCAAGAAGTTCTTTGAGTATGTTTTGCAA
genomic: AAACATCAATTCCTAGGAAGCATGGCCCTGCAATTGCTGGCTACGAGACGgtattatcac ... tgttctgtagGCCCTCAAGAAGTTCTTTGAGTATGTTTTGCAA
EST: gi|32825337|gb|CD965059.1|CD965059
EST:     AAACATCAATTCCTAGGAAGCATGGCCCTGCAATTGCTGGCTACGAGACG                         GCCCTCAAGAAGTTCTTTGAGTATGTTTTGCAA
genomic: AAACATCAATTCCTAGGAAGCATGGCCCTGCAATTGCTGGCTACGAGACGgtattatcac ... tgttctgtagGCCCTCAAGAAGTTCTTTGAGTATGTTTTGCAA
EST: gi|76016282|gb|DT943452.1|DT943452
EST:     AAACATCAATTCCTAGGAAGCATGGCCCTGCAATTGCTGGCTACGAGACG                         GCCCTCAAGAAGTTCTTTGAGTATGTTTTGCAA
genomic: AAACATCAATTCCTAGGAAGCATGGCCCTGCAATTGCTGGCTACGAGACGgtattatcac ... tgttctgtagGCCCTCAAGAAGTTCTTTGAGTATGTTTTGCAA

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: 47 (upstream exon), 33 (downstream exon)
Score: 65

CATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGGCCCTGCAATTGCTGGCTACGAGACGgtattatcac ... tgttctgtagGCCCTCAAGAAGTTCTTTGAGTATGTTTTGCAA


Block sizes: 49 (upstream exon), 33 (downstream exon)
Score: 73

CATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGGCCCTGCAATTGCTGGCTACGAGACGgtattatcac ... tgttctgtagGCCCTCAAGAAGTTCTTTGAGTATGTTTTGCAA


Block sizes: 47 (upstream exon), 33 (downstream exon)
Score: 136

CATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGGCCCTGCAATTGCTGGCTACGAGACGgtattatcac ... tgttctgtagGCCCTCAAGAAGTTCTTTGAGTATGTTTTGCAA


Block sizes: 47 (upstream exon), 33 (downstream exon)
Score: 69

CATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGGCCCTGCAATTGCTGGCTACGAGACGgtattatcac ... tgttctgtagGCCCTCAAGAAGTTCTTTGAGTATGTTTTGCAA