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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGATCAATCCCGCTGAGACCTTTGGGGATATTGTGATTGATTACCCgtaagatgcagtaacctttcatcgtgctgatttgtacttataaaacaaattgaagaaacataaaacccatcttgcag

Basic information

species Zea mays
transcript GRMZM2G023798_T02
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G023798_T01 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os02g04710.1 (Oryza sativa), 5'ss of exon 13
CTGATCAATCCCGCTGAGACCTTTGGGGATATTGTGATTGATTACCCgtaagatgcagtaacct-ttcatcgtgctgatttgtacttataaaacaaattgaagaaacataaaacccatcttgcag------------------------------
|| |||||||| ||||||||||||||||| |||||||||||||| ||||||||      ||||  | ||| || ||  ||| |   | |    ||  | ||||    |   | |     || |                                
CTTATCAATCCTGCTGAGACCTTTGGGGACATTGTGATTGATTATCCgtaagacattacaacccatccattgtcctcttttcttgctttgc--catgtagaaggtgaactgatctttctttccttctctcctttgtatgtgtataaaatttatag
















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|32837111|gb|CD976789.1|CD976789
EST:     CTGATCAATCCTGCTGAGACCTTTGGGGATATTGTGATTGATTACCC                         GTATGTTGAATGT
genomic: CTGATCAATCCCGCTGAGACCTTTGGGGATATTGTGATTGATTACCCgtaagatgca ... catcttgcagGTATGTTGAATGT
EST: gi|18659473|gb|BM500356.1|BM500356
EST:     CTGATCAATCCTGCTGAGACCTTTGGGGATATNGTGATTGATTACCC                         GTATGTTGAATGTACATCAGCAGCAATTCAGGNCCTGACATCATTCAAAAA
genomic: CTGATCAATCCCGCTGAGACCTTTGGGGATATTGTGATTGATTACCCgtaagatgca ... catcttgcagGTATGTTGAATGTACATCAGCAGCAATTCAGGCCCTGACATCATTCAAAAA
EST: gi|61118731|gb|DN559692.1|DN559692
EST:     CTGATCAATCCTGCTGAGACCTTTGGGGATATTGTGATTGATTACCC                         GTATGTTGAATGTACATCAGCAGCAATTCAGGCCCTGACATCATTCAAAAA
genomic: CTGATCAATCCCGCTGAGACCTTTGGGGATATTGTGATTGATTACCCgtaagatgca ... catcttgcagGTATGTTGAATGTACATCAGCAGCAATTCAGGCCCTGACATCATTCAAAAA
EST: gi|5566676|gb|AI881587.1|AI881587
EST:     CTGATCAATCCTGCTGAGACCTTTGGGGATATTGTGATTGATTACCC                         GTATGTTGAATGTACATCAGCAGCAATTCAGGCCCTGACATCATTCAAAAA
genomic: CTGATCAATCCCGCTGAGACCTTTGGGGATATTGTGATTGATTACCCgtaagatgca ... catcttgcagGTATGTTGAATGTACATCAGCAGCAATTCAGGCCCTGACATCATTCAAAAA
EST: gi|87156285|gb|DY401074.1|DY401074
EST:     CTGATCAATCCTGCTGAGACCTTTGGGGATATTGTGATTGATTACCC                         GTAATGT-GAATGTACATCAACAGCAATTCAGGCCCTGACATCATTCAAAA
genomic: CTGATCAATCCCGCTGAGACCTTTGGGGATATTGTGATTGATTACCCgtaagatgca ... catcttgcagGTA-TGTTGAATGTACATCAGCAGCAATTCAGGCCCTGACATCATTCAAAA

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: 195

CTGATCAATCCCGCTGAGACCTTTGGGGATATTGTGATTGATTACCCgtaagatgca ... catcttgcagGTATGTTGAATGTACATCAGCAGCAATTCAGGCCCTGACATCATTCAAAAAACTATACCCTGGGCACCGCAGGAAAGAGGTGGATAACTGTATCAGCAAA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 95

CTGATCAATCCCGCTGAGACCTTTGGGGATATTGTGATTGATTACCCgtaagatgca ... catcttgcagGTATGTTGAATGTACATCAGCAGCAATTCAGGCCCTGACATCATTCAAAAAACTATACCCTGGGCACCGCAGGAAAGAGGTGGATAACTGTATCAGCAAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 132

CTGATCAATCCCGCTGAGACCTTTGGGGATATTGTGATTGATTACCCgtaagatgca ... catcttgcagGTATGTTGAATGTACATCAGCAGCAATTCAGGCCCTGACATCATTCAAAAAACTATACCCTGGGCACCGCAGGAAAGAGGTGGATAACTGTATCAGCAAA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 153

CTGATCAATCCCGCTGAGACCTTTGGGGATATTGTGATTGATTACCCgtaagatgca ... catcttgcagGTATGTTGAATGTACATCAGCAGCAATTCAGGCCCTGACATCATTCAAAAAACTATACCCTGGGCACCGCAGGAAAGAGGTGGATAACTGTATCAGCAAA