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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCCTGGTGTTGATCCCAATGATCCATCTATTAAAGATTTGCTGGCATCATTGCACAGCCAGGGAGAGgtatgttcttttttgggttccagtgaaggtctctgtattgtgatgcaatgaaattcatgttgcctctagactatagcattgttcagcttcaccttgacta...

Basic information

species Zea mays
transcript GRMZM2G078663_T03
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G078663_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g13970.1 (Oryza sativa), 5'ss of exon 9
CTTCCTGGTGTTGATCCCAATGATCCATCTATTAAAGATTTGCTGGCATCATTGCACAGCCAGGGAGAGgtatgttcttttttgggttccagtgaaggtctctgtattgtgatgcaat---gaaattcatgttgcctctagactatagcattgttcagcttcaccttgacta-
|| ||||||||||| |||||||| || ||| | |||||||||||||||||||||||  | ||||| |||||||| | || | |    |       || |   ||  ||   ||  ||    |||  ||    | |   ||    ||   | | |  |   || |    ||   
CTCCCTGGTGTTGACCCCAATGACCCCTCTGTGAAAGATTTGCTGGCATCATTGCATGGGCAGGGCGAGgtatgcttttctctatcctttt----agattgttgagtttcaatcaaacttagaaggtctgagtacagttatgacattagactttctattgtccctcgtacctt

upper sequence: GRMZM2G078663_T03 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA16G23590.1 (Glycine max), 5'ss of exon 9
CTTCCTGGTGTTGATCCCAATGATCCATCTATTAAAGATTTGCTGGCATCATTGCACAGCCAGGGAGAGgtatgttcttttttgggttccagtgaaggtctctgtattgtgatgcaatgaaattca-tgttgcctctagactatagcattgttcagcttcaccttgacta---
|||||||| ||||| || |||||||||||| | |||||||||||||| || ||||| |  |||   |||||| ||| | ||||  |        |   ||  ||  ||   |   |||    |  | | || |     |   |||      || |||||||||| || ||   
CTTCCTGGGGTTGACCCAAATGATCCATCTGTCAAAGATTTGCTGGCTTCCTTGCAAAATCAGTCTGAGgtaggttttcttttatg----gaaaataatcattgagtttgaaaagaatctcttagaatatttcacagggggcatatttaaatttagcttcacctagattagcc
















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|50328322|gb|CO523448.1|CO523448
EST:     ATGATCCATCTATTAAAGATTTGCTGGCATCATTGCCCAGCCAGGGAGAG                         GAAGAGAAGAAGGAAGCCAAGTTAGACAAACCAGAAGACGAGAAGAACTGC
genomic: ATGATCCATCTATTAAAGATTTGCTGGCATCATTGCACAGCCAGGGAGAGgtatgttctt ... tcttaaacagGAAGAGAAGAAGGAAGACAAGTTAGACAAAACAGAAGACGAGAAGAACTGC
EST: gi|166653551|gb|EG277332.1|EG277332
EST:     TGATCCATCTATTAAAGATTTGCTGGCATCATTAGCACAGCCAGGGAGAG                         GAAGAGAAGAAGGAAGACAAGTTAGACAAAAC
genomic: TGATCCATCTATTAAAGATTTGCTGGCATCATT-GCACAGCCAGGGAGAGgtatgttctt ... tcttaaacagGAAGAGAAGAAGGAAGACAAGTTAGACAAAAC

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), 48 (downstream exon)
Score: 204

CTTCCTGGTGTTGATCCCAATGATCCATCTATTAAAGATTTGCTGGCATCATTGCACAGCCAGGGAGAGgtatgttctt ... tcttaaacagGAAGAGAAGAAGGAAGACAAGTTAGACAAAACAGAAGACGAGAAGAACTGCTTCAAGCTGGAGTGATGTCGCTGTGGTGCTTTTGTGACTGATCATCTCT


Block sizes: 46 (upstream exon), 45 (downstream exon)
Score: 72

CTTCCTGGTGTTGATCCCAATGATCCATCTATTAAAGATTTGCTGGCATCATTGCACAGCCAGGGAGAGgtatgttctt ... tcttaaacagGAAGAGAAGAAGGAAGACAAGTTAGACAAAACAGAAGACGAGAAGAACTGCTTCAAGCTGGAGTGATGTCGCTGTGGTGCTTTTGTGACTGATCATCTCT


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 82

CTTCCTGGTGTTGATCCCAATGATCCATCTATTAAAGATTTGCTGGCATCATTGCACAGCCAGGGAGAGgtatgttctt ... tcttaaacagGAAGAGAAGAAGGAAGACAAGTTAGACAAAACAGAAGACGAGAAGAACTGCTTCAAGCTGGAGTGATGTCGCTGTGGTGCTTTTGTGACTGATCATCTCT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 84

CTTCCTGGTGTTGATCCCAATGATCCATCTATTAAAGATTTGCTGGCATCATTGCACAGCCAGGGAGAGgtatgttctt ... tcttaaacagGAAGAGAAGAAGGAAGACAAGTTAGACAAAACAGAAGACGAGAAGAACTGCTTCAAGCTGGAGTGATGTCGCTGTGGTGCTTTTGTGACTGATCATCTCT