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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggaatcgccgctaccactggagctcctcctatggcgccgtcttttgacccgtctgctcaacaatcccctgatccgtttccctgcatctttcctctttctttatcgcagTTCAGCGACGTTCTTGGCAAGGGCGCGTCCAAGATTGT

Basic information

species Zea mays
transcript GRMZM2G034779_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G034779_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g38530.2 (Oryza sativa), 3'ss of exon 1
gtatggaatcgccgctaccactggagctcctcctatggcg-ccgtcttttgaccc-gtctgctcaacaatcccctgatccgtttccctgcatctttcctctttctttatcgcagTTCAGCGACGTTCTTGGCAAGGGCGCGTCCAAGATTGT
                   || | | |  |||||   ||  |||| | ||||  |  |||        |     |   ||   |  |||   | ||| | || || |   ||||| || |||||||||||||||||||||||||||||  ||
-----------------gtacggcaccatctccttcagcctccgtttcttgattctatcttgcttttgagttttta--ccagattgctgatccgttctttttgctgt---gcagTACAACGACGTTCTTGGCAAGGGCGCGTCCAAGACCGT
















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|211336034|gb|FL020964.1|FL020964
EST:     ACCCGTGCCCGGAGTATGCGGAGGTCGACCCCACCGGCCGGTACGGACGG                         TTCAGCGACGTTCTTGGCAAGGGCGCGTCCAAGATTGT
genomic: ACCCGTGCCCGGAGTATGCGGAGGTCGACCCCACCGGCCGGTACGGACGGgtatggaatc ... tttatcgcagTTCAGCGACGTTCTTGGCAAGGGCGCGTCCAAGATTGT
EST: gi|71764174|gb|DR962111.1|DR962111
EST:     ACCCGTGCCCGGAGTATGCGGAGGTCGACCCCACCGGCCGGTACGGACGG                         TTCAGCGACGTTCTTGGCAAGGGCGCGTCCAAGATTGT
genomic: ACCCGTGCCCGGAGTATGCGGAGGTCGACCCCACCGGCCGGTACGGACGGgtatggaatc ... tttatcgcagTTCAGCGACGTTCTTGGCAAGGGCGCGTCCAAGATTGT

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: 49 (upstream exon), 38 (downstream exon)
Score: 248

GCGAGCTAGAGCTGCAGGGATGATAAGCGCCAAGTCCAACGCCGCCGTGTACCCGTGCCCGGAGTATGCGGAGGTCGACCCCACCGGCCGGTACGGACGGgtatggaatc ... tttatcgcagTTCAGCGACGTTCTTGGCAAGGGCGCGTCCAAGATTGT


Block sizes: 49 (upstream exon), 38 (downstream exon)
Score: 71

GCGAGCTAGAGCTGCAGGGATGATAAGCGCCAAGTCCAACGCCGCCGTGTACCCGTGCCCGGAGTATGCGGAGGTCGACCCCACCGGCCGGTACGGACGGgtatggaatc ... tttatcgcagTTCAGCGACGTTCTTGGCAAGGGCGCGTCCAAGATTGT


Block sizes: 47 (upstream exon), 38 (downstream exon)
Score: 49

GCGAGCTAGAGCTGCAGGGATGATAAGCGCCAAGTCCAACGCCGCCGTGTACCCGTGCCCGGAGTATGCGGAGGTCGACCCCACCGGCCGGTACGGACGGgtatggaatc ... tttatcgcagTTCAGCGACGTTCTTGGCAAGGGCGCGTCCAAGATTGT


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 178

GCGAGCTAGAGCTGCAGGGATGATAAGCGCCAAGTCCAACGCCGCCGTGTACCCGTGCCCGGAGTATGCGGAGGTCGACCCCACCGGCCGGTACGGACGGgtatggaatc ... tttatcgcagTTCAGCGACGTTCTTGGCAAGGGCGCGTCCAAGATTGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctcaacaatcccctgatccgtttccctgcatctttcctctttctttatcgcagTTCAGCGACGTTCTTGGCAAGGGCGCGTCCAAGATTGT
            ccctgat  putative branch site (score: 178)
          tcccctgatccgtttc  CT-rich tract
                                         tttctttat  TA-rich tract