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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcagatgtgtcatcacaatcgcagcatattgctggggaaaacggtgcagttagcacgctcgtttcggctgatcctctgacctttgtcatctttctggcagGCCAGCGGAAGCTGTCACAGTCGTCGATTTTAGTTGTTGGGGCTGGAGGTTTGGGCTCTCCCCTGGCATTGTATCTAGCAGCTTGTGGTGTCG

Basic information

species Zea mays
transcript GRMZM2G160842_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G160842_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g32460.1 (Oryza sativa), 3'ss of exon 1
tcagatgtgtcatcacaatcgcagcatattgctggggaaaacggtgcagttagcacgctcgtttcggctgatcctctgaccttt-gtcatctttctggcagGCCAGCGGAAGCTGTCACAGTCGTCGATTTTAGTTGTTGGGGCTGGAGGTTTGGGCTCTCCCCTGGCATTGTATCTAGCAGCTTGTGGTGTCG
                || | |||| |  |           || |   || |||     |||   ||    ||   |||| ||| || | || | | ||||||||||| ||||| || ||||| |||||||| || || || |||||||| |||||||| ||| ||||| |||| ||||||||||||||||| |
-------------gttaagctcagc-tgctcacacatggcgcgttatcgt-agcctcagcgtagtggagactctagtgactttttgttagctatgtcgcagGCCAGCGTAAGCTCTCGCAGTCATCGATTTTGGTGGTGGGCGCTGGAGGATTGGGCTCGCCCGTGGCACTGTACCTAGCAGCTTGTGGTGTTG
















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|211107289|gb|FL028196.1|FL028196
EST:     GATCTACCGGTACAGCCGCCACCTCCTTCTCCCGGACTTCGGGGTCGAAG                         GCCAGCGGAAGCTATCACAGTCGTCGATTTTAGTTGTTGGGGCTGGAGGTT
genomic: GATCTACCGGTACAGCCGCCACCTCCTTCTCCCGGACTTCGGGGTCGAAGgtcagttgtt ... tttctggcagGCCAGCGGAAGCTGTCACAGTCGTCGATTTTAGTTGTTGGGGCTGGAGGTT
EST: gi|211315595|gb|FL072344.1|FL072344
EST:     GATCTACCGGTACAGCCGCCACCTCCTTCTCCCGGACTTCGGGGTCGAAG                         GCCAGCGGAAGCTGTCACAGTCGTCGA
genomic: GATCTACCGGTACAGCCGCCACCTCCTTCTCCCGGACTTCGGGGTCGAAGgtcagttgtt ... tttctggcagGCCAGCGGAAGCTGTCACAGTCGTCGA
EST: gi|211108194|gb|FL028200.1|FL028200
EST:     GATCTACCGGTACAGCCGCCACCTCCTTCTCCCGGACTTCGGGGTCGAAG                         GCCAGCGGAAGCTATCACAGTCGTCGATTTTAGTTGTTGGGGCTGGAGGTT
genomic: GATCTACCGGTACAGCCGCCACCTCCTTCTCCCGGACTTCGGGGTCGAAGgtcagttgtt ... tttctggcagGCCAGCGGAAGCTGTCACAGTCGTCGATTTTAGTTGTTGGGGCTGGAGGTT
EST: gi|211315592|gb|FL072341.1|FL072341
EST:     GATCTACCGGTACAGCCGCCACCTCCTTCTCCCGGACTTCGGGGTCGAAG                         GCCAGCGGAAGCTATCACAGTCGTCGATTTTAGTTGTTG
genomic: GATCTACCGGTACAGCCGCCACCTCCTTCTCCCGGACTTCGGGGTCGAAGgtcagttgtt ... tttctggcagGCCAGCGGAAGCTGTCACAGTCGTCGATTTTAGTTGTTG
EST: gi|37423894|gb|CF649677.1|CF649677
EST:     GATCTACCGGTACAGCCGCCACCTCCTTCTCCCGGACTTCGGGGTCGAAG                         GCCAGCGGAAGCTGTCACAGTCGTCGATTTTAGTTGTTGGGGCTGGAGGTT
genomic: GATCTACCGGTACAGCCGCCACCTCCTTCTCCCGGACTTCGGGGTCGAAGgtcagttgtt ... tttctggcagGCCAGCGGAAGCTGTCACAGTCGTCGATTTTAGTTGTTGGGGCTGGAGGTT
EST: gi|211107290|gb|FL028197.1|FL028197
EST:     GATCTACCGGTACAGCCGCCACCTCCTTCTCCCGGACTTCGGGGTCGAAG                         GCCAGCGGAAGCTGTCACAKTCGTCGATTTTAGTTGTTGGGGCTGGAGGTT
genomic: GATCTACCGGTACAGCCGCCACCTCCTTCTCCCGGACTTCGGGGTCGAAGgtcagttgtt ... tttctggcagGCCAGCGGAAGCTGTCACAGTCGTCGATTTTAGTTGTTGGGGCTGGAGGTT
EST: gi|149009441|gb|EE041457.2|EE041457
EST:     GATCTACCGGTACAGCCGCCACCTCCTTCTCCCGGACTTCGGGGTCGAAG                         GCCAGCGGAAGCTGTCACAGTCGTCGATTTTAGTTGTTGGGGCTGGAGGTT
genomic: GATCTACCGGTACAGCCGCCACCTCCTTCTCCCGGACTTCGGGGTCGAAGgtcagttgtt ... tttctggcagGCCAGCGGAAGCTGTCACAGTCGTCGATTTTAGTTGTTGGGGCTGGAGGTT
EST: gi|211107292|gb|FL028199.1|FL028199
EST:     GATCTACCGGTACAGCCGCCACCTCCTTCTCCCGGACTTCGGGGTCGAAG                         GCCAGCGGAAGCTGTCACAGTCGTCGATTTTAGTTGTTGGGGCTGGAGGTT
genomic: GATCTACCGGTACAGCCGCCACCTCCTTCTCCCGGACTTCGGGGTCGAAGgtcagttgtt ... tttctggcagGCCAGCGGAAGCTGTCACAGTCGTCGATTTTAGTTGTTGGGGCTGGAGGTT
EST: gi|211108195|gb|FL028201.1|FL028201
EST:     GATCTACCGGTACAGCCGCCACCTCCTTCTCCCGGACTTCGGGGTCGAAG                         GCCAGCGGAAGCTGTCACAGTCGTCGATTTTAGTTGTTGGGGCTGGAGGTT
genomic: GATCTACCGGTACAGCCGCCACCTCCTTCTCCCGGACTTCGGGGTCGAAGgtcagttgtt ... tttctggcagGCCAGCGGAAGCTGTCACAGTCGTCGATTTTAGTTGTTGGGGCTGGAGGTT
EST: gi|148954835|gb|EC900308.2|EC900308
EST:     GATCTACCGGTACAGCCGCCACCTCCTTCTCCCGGACTTCGGGGTCGAAG                         GCCAGCGGAAGCTGTCACAGTCGTCGATTTTAGTTGTTGGGGCTGGAGGTT
genomic: GATCTACCGGTACAGCCGCCACCTCCTTCTCCCGGACTTCGGGGTCGAAGgtcagttgtt ... tttctggcagGCCAGCGGAAGCTGTCACAGTCGTCGATTTTAGTTGTTGGGGCTGGAGGTT
EST: gi|89761475|gb|DY689476.1|DY689476
EST:     GATCTACCGGTACAGCCGCCACCTCCTTCTCCCGGACTTCGGGGTCGAAG                         GCCAGCGGAAGCTGTCACAGTCGTCGATTTTAGTTGTTGGGGCTGGAGGTT
genomic: GATCTACCGGTACAGCCGCCACCTCCTTCTCCCGGACTTCGGGGTCGAAGgtcagttgtt ... tttctggcagGCCAGCGGAAGCTGTCACAGTCGTCGATTTTAGTTGTTGGGGCTGGAGGTT
EST: gi|211107291|gb|FL028198.1|FL028198
EST:     GATCTACCGGTACAGCCGCCACCTCCTTCTCCCGGACTTCGGGGTCGAAG                         GCCAGCGGAAGCTATCACAGTCGTCGATTTTAGTTGTTGGGGCTGGAGGTT
genomic: GATCTACCGGTACAGCCGCCACCTCCTTCTCCCGGACTTCGGGGTCGAAGgtcagttgtt ... tttctggcagGCCAGCGGAAGCTGTCACAGTCGTCGATTTTAGTTGTTGGGGCTGGAGGTT

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), 49 (downstream exon)
Score: 313

AGCCGCGTGGGTAACGAGTTTGCTCCGGACGGTAGCCTCCCGGCGGATATGATCTACCGGTACAGCCGCCACCTCCTTCTCCCGGACTTCGGGGTCGAAGgtcagttgtt ... tttctggcagGCCAGCGGAAGCTGTCACAGTCGTCGATTTTAGTTGTTGGGGCTGGAGGTTTGGGCTCTCCCCTGGCATTGTATCTAGCAGCTTGTGGTGTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 179

AGCCGCGTGGGTAACGAGTTTGCTCCGGACGGTAGCCTCCCGGCGGATATGATCTACCGGTACAGCCGCCACCTCCTTCTCCCGGACTTCGGGGTCGAAGgtcagttgtt ... tttctggcagGCCAGCGGAAGCTGTCACAGTCGTCGATTTTAGTTGTTGGGGCTGGAGGTTTGGGCTCTCCCCTGGCATTGTATCTAGCAGCTTGTGGTGTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 247

AGCCGCGTGGGTAACGAGTTTGCTCCGGACGGTAGCCTCCCGGCGGATATGATCTACCGGTACAGCCGCCACCTCCTTCTCCCGGACTTCGGGGTCGAAGgtcagttgtt ... tttctggcagGCCAGCGGAAGCTGTCACAGTCGTCGATTTTAGTTGTTGGGGCTGGAGGTTTGGGCTCTCCCCTGGCATTGTATCTAGCAGCTTGTGGTGTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 249

AGCCGCGTGGGTAACGAGTTTGCTCCGGACGGTAGCCTCCCGGCGGATATGATCTACCGGTACAGCCGCCACCTCCTTCTCCCGGACTTCGGGGTCGAAGgtcagttgtt ... tttctggcagGCCAGCGGAAGCTGTCACAGTCGTCGATTTTAGTTGTTGGGGCTGGAGGTTTGGGCTCTCCCCTGGCATTGTATCTAGCAGCTTGTGGTGTCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcagttagcacgctcgtttcggctgatcctctgacctttgtcatctttctggcagGCCAGCGGAAGCTGTCACAGTCGTCGATTTTAGTTGTTGGGGCTGGAGGTTTGGGCTCTCCCCTGGCATTGTATCTAGCAGCTTGTGGTGTCG
                            ctctgac  putative branch site (score: 249)
                                  cctttgtcatctttct  CT-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcagatgtgtcatcacaatcgcagcatattgctggggaaaacggtgcagttagcacgctcgtttcggctgatcctctgacctttgtcatctttctggcagGCCAGCGGAAGCTGTCACAGTCGTCGATTTTAGTTGTTGGGGCTGGAGGTTTGGGCTCTCCCCTGGCATTGTATCTAGCAGCTTGTGGTGTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT