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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACCTGTGCCCGGAGCCGTACGCGGAGGAGAACGCGCGGTTCCTGCGCACGAACGGGATCCGGCTTCACCAGTTCGCCGTCGAAGGGAGCAAGgtacgagaaccacatttgacaccgtctcttttcagtctcggcaacacaaacatttggtacgtgctagcgtaacagtggcgcacaacaagagcttctgtgt...

Basic information

species Zea mays
transcript GRMZM2G126765_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G126765_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g53160.1 (Oryza sativa), 5'ss of exon 2
GTACCTGTGCCCGGAGCCGTACGCGGAGGAGAACGCGCGGTTCCTGCGCACGAACGGGATCCGGCTTCACCAGTTCGCCGTCGAAGGGAGCAAGgtacgagaaccacatttgacaccgtctcttttcagtctcggcaacacaaac---atttggtacgtgctagcgtaacagtggcgcacaacaagagcttctgtgt
|||||||||||||||||||||| ||||||||||| ||||||| |||     |||||| |||  ||||||||||||||   | || || |||||||||   |||| |  |   | | | | |   || ||||     |       |   ||||   ||| | | ||  |   |     | || | |    || | || 
GTACCTGTGCCCGGAGCCGTACCCGGAGGAGAACACGCGGTTTCTGGAGCAGAACGGCATCAAGCTTCACCAGTTCGGTATTGACGGCAGCAAGgtaaatgaacaa-gtcaaaaatcatatgcgttgagtcctttgattttctgctttattttccacg-gatggcaaagtcgatcttcgcatcgaattgttttttg-
















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|18174219|gb|BM349607.1|BM349607
EST:     TGCGCACGAACGGGATCCGGCTTCACCAGTTCGCCGTCGAAGGGAGCAAG                         AGTGGTCCGACAGTGCTGGATACCATGTCGGCGCAGGAACCATTCGTCCAC
genomic: TGCGCACGAACGGGATCCGGCTTCACCAGTTCGCCGTCGAAGGGAGCAAGgtacgagaac ... ttatccacagAGTGGTCCGACAGTGCTGGATACCATGTCGGCGCAGGAACCATTCGTCCAC
EST: gi|31558116|gb|CD527328.1|CD527328
EST:     TGCGCACGAACGGGATCCGGCTTCACCAGTTCGCCGTCGAAGGGAGCAAG                         AGTGGTCCGACAGTGCTGGATACCATGTCGGCGCAGGAACCATTCGTCCAC
genomic: TGCGCACGAACGGGATCCGGCTTCACCAGTTCGCCGTCGAAGGGAGCAAGgtacgagaac ... ttatccacagAGTGGTCCGACAGTGCTGGATACCATGTCGGCGCAGGAACCATTCGTCCAC
EST: gi|31558117|gb|CD527329.1|CD527329
EST:     TGCGCACGAACGGGATCCGGCTTCACCAGTTCGCCGTCGAAGGGAGCAAG                         AGTGGTCCGACAGTGCTGGATACCATGTCGGCGCAGGAACCATTCGTCCAC
genomic: TGCGCACGAACGGGATCCGGCTTCACCAGTTCGCCGTCGAAGGGAGCAAGgtacgagaac ... ttatccacagAGTGGTCCGACAGTGCTGGATACCATGTCGGCGCAGGAACCATTCGTCCAC
EST: gi|211128137|gb|FL366473.1|FL366473
EST:     TGCGCACGAACGGGATCCGCCTTCACCAGTTCGCCGTCGAAGGGAGCAAG                         AGTGGTCCGACAGTGCTGGATACCATGTCGGCGCAGGAACCATTCGTCCAC
genomic: TGCGCACGAACGGGATCCGGCTTCACCAGTTCGCCGTCGAAGGGAGCAAGgtacgagaac ... ttatccacagAGTGGTCCGACAGTGCTGGATACCATGTCGGCGCAGGAACCATTCGTCCAC
EST: gi|78093024|gb|DV521398.1|DV521398
EST:     TGCGCACGAACGGGATCCGGCTTCACCAGTTCGCCGTCGAAGGGAGCAAG                         AGTGGTCCGACAGTGCTGGATACCATGTCGGCGCAGGAACCATTCGTCCAC
genomic: TGCGCACGAACGGGATCCGGCTTCACCAGTTCGCCGTCGAAGGGAGCAAGgtacgagaac ... ttatccacagAGTGGTCCGACAGTGCTGGATACCATGTCGGCGCAGGAACCATTCGTCCAC
EST: gi|18166488|gb|BM336327.1|BM336327
EST:     CACCAGTTCGCCGTCGAAGGGAGCAAG                         AGTGGTCCGACAGTGCTGGATACCATGTCGGCGCAGGAACCATTCGTCCAC
genomic: CACCAGTTCGCCGTCGAAGGGAGCAAGgtacgagaac ... ttatccacagAGTGGTCCGACAGTGCTGGATACCATGTCGGCGCAGGAACCATTCGTCCAC
EST: gi|37388689|gb|CF631556.1|CF631556
EST:     TTCACCAGTTCGCCGTCGAAGGGAGCAAG                         AGTGGTCCGACAGTGCTGGATACCATGTCGGCGCAGGAACCATTCGTCCAC
genomic: TTCACCAGTTCGCCGTCGAAGGGAGCAAGgtacgagaac ... ttatccacagAGTGGTCCGACAGTGCTGGATACCATGTCGGCGCAGGAACCATTCGTCCAC
EST: gi|211166824|gb|FL324152.1|FL324152
EST:     TGCGCACGAACGGGATCCGCCTTCACCAGTTCGCCGTCGAAGGGAGCAAG                         AGTGGTCCGACAGTGCTGGATACCATGTCGGCGC
genomic: TGCGCACGAACGGGATCCGGCTTCACCAGTTCGCCGTCGAAGGGAGCAAGgtacgagaac ... ttatccacagAGTGGTCCGACAGTGCTGGATACCATGTCGGCGC
EST: gi|211055639|gb|FL339119.1|FL339119
EST:     TGCGCACGAACGGGATCCGCCTTCACCAGTTCGCCGTCGAANGGAGCAAG                         AGTGGTCCGACAGTGCTGGAT
genomic: TGCGCACGAACGGGATCCGGCTTCACCAGTTCGCCGTCGAAGGGAGCAAGgtacgagaac ... ttatccacagAGTGGTCCGACAGTGCTGGAT
EST: gi|17929863|gb|BM266823.1|BM266823
EST:     TGCGCACGAACGGGATCCGGCTTCACCAGTTCGCCGTCGAAGGGAGCAAG                         AGTGGTCCGACAGTGCTGGATACCATGTCGGCGCAGGAACCATTCGTCCAC
genomic: TGCGCACGAACGGGATCCGGCTTCACCAGTTCGCCGTCGAAGGGAGCAAGgtacgagaac ... ttatccacagAGTGGTCCGACAGTGCTGGATACCATGTCGGCGCAGGAACCATTCGTCCAC
EST: gi|18162825|gb|BM332664.1|BM332664
EST:     CGCACGAACGGGATCCGGCTTCACCAGTTCGCCGTCGAAGGGAGCAAG                         AGTGGTCCGACAGTGCTGGATACCATGTCGGCGCAGGAACCATTCGTCCAC
genomic: CGCACGAACGGGATCCGGCTTCACCAGTTCGCCGTCGAAGGGAGCAAGgtacgagaac ... ttatccacagAGTGGTCCGACAGTGCTGGATACCATGTCGGCGCAGGAACCATTCGTCCAC
EST: gi|17930139|gb|BM267099.1|BM267099
EST:     CGCACGAACGGGATCCGGCTTCACCAGTTCGCCGTCGAA-GGAGCAAAG                         AGTGGTCCGACAGTGCTGGATACCATGTCGGCGCAGGAACCATTCGTCCA
genomic: CGCACGAACGGGATCCGGCTTCACCAGTTCGCCGTCGAAGGGAGC-AAGgtacgagaac ... ttatccacagAGTGGTCCGACAGTGCTGGATACCATGTCGGCGCAGGAACCATTCGTCCA
EST: gi|16920825|gb|BM074849.1|BM074849
EST:     TGCGCACGAACGGGATCCGGCTTCACCAGTTCGCCGTCGAAGGGAGCAAG                         AGTGGTCCGACAGTGCTGGATACCATGTCGGCGCAGGAACCATTCGTCCAC
genomic: TGCGCACGAACGGGATCCGGCTTCACCAGTTCGCCGTCGAAGGGAGCAAGgtacgagaac ... ttatccacagAGTGGTCCGACAGTGCTGGATACCATGTCGGCGCAGGAACCATTCGTCCAC
EST: gi|18167487|gb|BM337326.1|BM337326
EST:     TGCGCACGAACGGGATCCGGCTTCACCAGTTCGCCGTCGAAGGGAGCAAG                         AGTGGTCCGACAGTGCTGGATACCATGTCGGCGCAGGAACCATTCGTCCAC
genomic: TGCGCACGAACGGGATCCGGCTTCACCAGTTCGCCGTCGAAGGGAGCAAGgtacgagaac ... ttatccacagAGTGGTCCGACAGTGCTGGATACCATGTCGGCGCAGGAACCATTCGTCCAC
EST: gi|76283506|gb|DV023074.1|DV023074
EST:     TGCGCACGAACGGGATCCGGCTTCACCAGTTCGCCGTCGAAGGGAGCAAG                         AGTGGTCCGACAGTGCTGGATACCATGTCGGCGCAGGAACCATTCGTCCAC
genomic: TGCGCACGAACGGGATCCGGCTTCACCAGTTCGCCGTCGAAGGGAGCAAGgtacgagaac ... ttatccacagAGTGGTCCGACAGTGCTGGATACCATGTCGGCGCAGGAACCATTCGTCCAC
EST: gi|78093023|gb|DV521397.1|DV521397
EST:     TGCGCACGAACGGGATCCGGCTTCACCAGTTCGCCGTCGAAGGGAGCAAG                         AGTGGTCCGACAGTGCTGGATACCATGTCGGCGCAGGAACCATTCGTCCAC
genomic: TGCGCACGAACGGGATCCGGCTTCACCAGTTCGCCGTCGAAGGGAGCAAGgtacgagaac ... ttatccacagAGTGGTCCGACAGTGCTGGATACCATGTCGGCGCAGGAACCATTCGTCCAC

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: 48 (upstream exon), 46 (downstream exon)
Score: 40

GTACCTGTGCCCGGAGCCGTACGCGGAGGAGAACGCGCGGTTCCTGCGCACGAACGGGATCCGGCTTCACCAGTTCGCCGTCGAAGGGAGCAAGgtacgagaac ... ttatccacagAGTGGTCCGACAGTGCTGGATACCATGTCGGCGCAGGAACCATTCGTCCACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 31

GTACCTGTGCCCGGAGCCGTACGCGGAGGAGAACGCGCGGTTCCTGCGCACGAACGGGATCCGGCTTCACCAGTTCGCCGTCGAAGGGAGCAAGgtacgagaac ... ttatccacagAGTGGTCCGACAGTGCTGGATACCATGTCGGCGCAGGAACCATTCGTCCACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTG


Block sizes: 43 (upstream exon), 48 (downstream exon)
Score: 30

GTACCTGTGCCCGGAGCCGTACGCGGAGGAGAACGCGCGGTTCCTGCGCACGAACGGGATCCGGCTTCACCAGTTCGCCGTCGAAGGGAGCAAGgtacgagaac ... ttatccacagAGTGGTCCGACAGTGCTGGATACCATGTCGGCGCAGGAACCATTCGTCCACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTG


Block sizes: 30 (upstream exon), 20 (downstream exon)
Score: 3

GTACCTGTGCCCGGAGCCGTACGCGGAGGAGAACGCGCGGTTCCTGCGCACGAACGGGATCCGGCTTCACCAGTTCGCCGTCGAAGGGAGCAAGgtacgagaac ... ttatccacagAGTGGTCCGACAGTGCTGGATACCATGTCGGCGCAGGAACCATTCGTCCACATCCCCGAAGAAACGATCCGGGAGGCGCTCAAAGTTGTCCTTG


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTACCTGTGCCCGGAGCCGTACGCGGAGGAGAACGCGCGGTTCCTGCGCACGAACGGGATCCGGCTTCACCAGTTCGCCGTCGAAGGGAGCAAGgtacgagaaccacatttgacaccgtctcttttcagtctcggcaacacaaacatttggtacgtgctagcgtaacagtggcgcacaacaagagcttctgtgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacaagag