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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgtcccctgatttgcttaagttataatttcctttctttaaaataatgactctcttcactatccaagctgctgtatgctaattagttcctcttacttgctgctagTGCTTCTTCCCACAAGAAGTTGCAAAAAGCATCACCACCCCGATGTTTATACTCAATCCAGCATATGATGTTTGGCAG

Basic information

species Zea mays
transcript GRMZM2G016561_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G016561_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g74330.1 (Oryza sativa), 3'ss of exon 6
gttgtcccctgatt-tgcttaagttataatttcctttctttaaaataatgactctctt------cactatccaagctgctgtatgctaattagttcctcttacttg---ctgctagTGCTTCTTCCCACAAGAAGTTGCAAAAAGCATCACCACCCCGATGTTTATACTCAATCCAGCATATGATGTTTGGCAG
||  |||  |  || |  ||| | ||   |||| | | || | |  |    || | ||       ||| | ||||||| | | |||||| |||     |||| | |   ||  |||||||| |||||||||||||| || ||| ||||||||||||| |||||||| |||||||||||||||||||||||||||
gtaatcctttagttgtttttatgatactgtttcttgtattaatatcatcaccttttttattcagtacttttcaagctgttatgtgctaagtagcaatccttaatcgtgccttgtagTGCTTTTTCCCACAAGAAGTGGCGAAAGGCATCACCACCCCAATGTTTATTCTCAATCCAGCATATGATGTTTGGCAG
















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|149085716|gb|EE175235.2|EE175235
EST:     ATGTGCGTAAAATATTCCCTCATTGCAGCTCAGATATGGAACCGGGGCAG                         TGCTTCTTCCCACAAGAAGTTGCAAAAAGCATCACCACCCCGATGTTTATA
genomic: ATGTGCGTAAAATATTCCCTCATTGCAGCTCAGATATGGAACCGGGGCAGgttgtcccct ... ttgctgctagTGCTTCTTCCCACAAGAAGTTGCAAAAAGCATCACCACCCCGATGTTTATA
EST: gi|78112623|gb|DV531017.1|DV531017
EST:     ATGTGCGTAAAATATTCCCTCATTGCAGCTCAGATATGGAACCGGGGCAG                         TGCTTCTTCCCACAAGAAGTTGCAAAAAGCATCACCACCCCGATGTTTATA
genomic: ATGTGCGTAAAATATTCCCTCATTGCAGCTCAGATATGGAACCGGGGCAGgttgtcccct ... ttgctgctagTGCTTCTTCCCACAAGAAGTTGCAAAAAGCATCACCACCCCGATGTTTATA
EST: gi|71426622|gb|DR807672.1|DR807672
EST:     ATGTGCGTAAAATATTCCCTCATTGCAGCTCAGATATGGAACCGGGGCAG                         TGCTTCTTCCCACAAGAAGTTGCAAAAAGCATCACCACCCCGATGTTTATA
genomic: ATGTGCGTAAAATATTCCCTCATTGCAGCTCAGATATGGAACCGGGGCAGgttgtcccct ... ttgctgctagTGCTTCTTCCCACAAGAAGTTGCAAAAAGCATCACCACCCCGATGTTTATA

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: 44 (upstream exon), 49 (downstream exon)
Score: 69

GATGTGCGTAAAATATTCCCTCATTGCAGCTCAGATATGGAACCGGGGCAGgttgtcccct ... ttgctgctagTGCTTCTTCCCACAAGAAGTTGCAAAAAGCATCACCACCCCGATGTTTATACTCAATCCAGCATATGATGTTTGGCAG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 35

GATGTGCGTAAAATATTCCCTCATTGCAGCTCAGATATGGAACCGGGGCAGgttgtcccct ... ttgctgctagTGCTTCTTCCCACAAGAAGTTGCAAAAAGCATCACCACCCCGATGTTTATACTCAATCCAGCATATGATGTTTGGCAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 79

GATGTGCGTAAAATATTCCCTCATTGCAGCTCAGATATGGAACCGGGGCAGgttgtcccct ... ttgctgctagTGCTTCTTCCCACAAGAAGTTGCAAAAAGCATCACCACCCCGATGTTTATACTCAATCCAGCATATGATGTTTGGCAG


Block sizes: 43 (upstream exon), 44 (downstream exon)
Score: 47

GATGTGCGTAAAATATTCCCTCATTGCAGCTCAGATATGGAACCGGGGCAGgttgtcccct ... ttgctgctagTGCTTCTTCCCACAAGAAGTTGCAAAAAGCATCACCACCCCGATGTTTATACTCAATCCAGCATATGATGTTTGGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcttcactatccaagctgctgtatgctaattagttcctcttacttgctgctagTGCTTCTTCCCACAAGAAGTTGCAAAAAGCATCACCACCCCGATGTTTATACTCAATCCAGCATATGATGTTTGGCAG
                                   ttcctcttacttgct  CT-rich tract
                            taattagtt  TA-rich tract