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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caattctggtcagaattccagtgctggaaattttagtctagcttgtagcagggcagtgctggtaatggttgatgcttacttcttgtgataaccattacagTGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAG

Basic information

species Zea mays
transcript GRMZM2G160569_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G160569_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g44070.2 (Oryza sativa), 3'ss of exon 1
-------caattctggtcagaattccagtgctggaaattttagtctagcttgtagcagggcagtgctggtaatggttgatgcttacttcttgtgataaccattacagTGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAG
        |||||||   | ||||      |   || |||   | | |||| ||||||||  | | ||| ||   | ||||    |||  | || | | |||  |||| ||||||||||| ||||||||||| || ||||| ||| |||||||||||||||| |||||||||||||| |||||| | |||
gtatcataaattctga--ataatttggaccc---aagtttccattt-gcttatagcagggttg-gttggcaaatctcgatgacagctttctttgtttatcatggcagTATGCTTGGATGGGAGCTTACCAGGGTATCACCTACACCGAGGGTTTGGATCAGGGGCAAACAGTTGGCTTGTCAATTTGGAG

upper sequence: GRMZM2G160569_T02 (Zea mays), 3'ss of exon 1
lower sequence: Vv05s0020g01110.t01 (Vitis vinifera), 3'ss of exon 1
caattctggtc-agaattccagtgctggaaattttagtctagcttgtagcagggcagtgctggtaatggttgatgcttacttcttgtgataaccat-tacagTGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAG
 ||  |||||| ||   |  |||  |||  ||| |   ||  ||  ||| |   |||      || |  |   | |||     || || |    ||   |||| ||| |||||||||  ||||| ||||||||||||||| | || | ||| ||||| ||||| ||||||||| |  || | |||
-aaagctggtccagtggtttagttttggttattgtgagctttctcatagtaaatcagaaagcata-ttataccttcttgacctttctgttctgtatgcgcagTATGCCTGGATGGAACATTACCTGGTTACCACCTCCACCGGGGATATGGGTCAGGGGCAAATAGTTGGCTCATTCATTTGGAG
















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|211148214|gb|FL118142.1|FL118142
EST:     CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGG                         TGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
genomic: CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGGgtaattcctc ... accattacagTGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
EST: gi|78085961|gb|DV514354.1|DV514354
EST:     AGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGG                         TGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
genomic: CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGGgtaattcctc ... accattacagTGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
EST: gi|76020752|gb|DT947922.1|DT947922
EST:     CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGG                         TGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
genomic: CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGGgtaattcctc ... accattacagTGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
EST: gi|211148217|gb|FL118145.1|FL118145
EST:     CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGG                         TGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
genomic: CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGGgtaattcctc ... accattacagTGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
EST: gi|31358086|gb|CD442443.1|CD442443
EST:     CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGG                         TGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
genomic: CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGGgtaattcctc ... accattacagTGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
EST: gi|91051275|gb|EB161693.1|EB161693
EST:     CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGG                         TGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
genomic: CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGGgtaattcctc ... accattacagTGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
EST: gi|29167875|gb|CB411135.1|CB411135
EST:     CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGG                         TGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
genomic: CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGGgtaattcctc ... accattacagTGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
EST: gi|67013089|gb|CO441838.1|CO441838
EST:     CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGG                         TGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
genomic: CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGGgtaattcctc ... accattacagTGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
EST: gi|149110301|gb|EE190341.2|EE190341
EST:     CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGG                         TGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
genomic: CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGGgtaattcctc ... accattacagTGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
EST: gi|211148215|gb|FL118143.1|FL118143
EST:     CGTCTTCGTCGGCCTCACGCTCATCCAGTCRGCGGCGGCCAAGGGAGCGG                         TGTGCTTGGATGGAAGC
genomic: CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGGgtaattcctc ... accattacagTGTGCTTGGATGGAAGC
EST: gi|31910847|gb|CD651628.1|CD651628
EST:     CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGG                         TGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
genomic: CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGGgtaattcctc ... accattacagTGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
EST: gi|76932741|gb|DV173142.1|DV173142
EST:     CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGG                         TGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
genomic: CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGGgtaattcctc ... accattacagTGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
EST: gi|149014463|gb|EE044079.2|EE044079
EST:     CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGG                         TGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
genomic: CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGGgtaattcctc ... accattacagTGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
EST: gi|148980469|gb|EE027156.2|EE027156
EST:     CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGG                         TGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
genomic: CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGGgtaattcctc ... accattacagTGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
EST: gi|31356050|gb|CD440407.1|CD440407
EST:     CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGG                         TGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
genomic: CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGGgtaattcctc ... accattacagTGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
EST: gi|211148212|gb|FL118140.1|FL118140
EST:     CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGNGGNCAAGGGAGCGG                         TGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
genomic: CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGGgtaattcctc ... accattacagTGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
EST: gi|93016717|gb|EB642237.1|EB642237
EST:     CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGG                         TGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
genomic: CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGGgtaattcctc ... accattacagTGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
EST: gi|50332178|gb|CO527304.1|CO527304
EST:     CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGG                         TGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
genomic: CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGGgtaattcctc ... accattacagTGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
EST: gi|149066716|gb|EE286857.2|EE286857
EST:     CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGG                         TGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
genomic: CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGGgtaattcctc ... accattacagTGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
EST: gi|61119158|gb|DN560119.1|DN560119
EST:     CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGG                         TGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
genomic: CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGGgtaattcctc ... accattacagTGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
EST: gi|32837292|gb|CD976970.1|CD976970
EST:     CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGG                         TGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
genomic: CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGGgtaattcctc ... accattacagTGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
EST: gi|149085225|gb|EE174733.2|EE174733
EST:     CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGG                         TGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
genomic: CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGGgtaattcctc ... accattacagTGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
EST: gi|211148219|gb|FL118147.1|FL118147
EST:     CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGG                         TGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
genomic: CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGGgtaattcctc ... accattacagTGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
EST: gi|148953388|gb|EE152882.2|EE152882
EST:     CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGG                         TGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
genomic: CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGGgtaattcctc ... accattacagTGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
EST: gi|149028342|gb|EE286117.2|EE286117
EST:     CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGG                         TGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
genomic: CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGGgtaattcctc ... accattacagTGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
EST: gi|149101142|gb|EE187250.2|EE187250
EST:     CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGG                         TGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
genomic: CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGGgtaattcctc ... accattacagTGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
EST: gi|211148221|gb|FL118149.1|FL118149
EST:     CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGG                         TGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
genomic: CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGGgtaattcctc ... accattacagTGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
EST: gi|78075695|gb|DV504129.1|DV504129
EST:     CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGG                         TGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
genomic: CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGGgtaattcctc ... accattacagTGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
EST: gi|211149659|gb|FL118150.1|FL118150
EST:     CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGG                         TGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
genomic: CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGGgtaattcctc ... accattacagTGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
EST: gi|149009227|gb|EE041332.2|EE041332
EST:     CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGG                         TGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT
genomic: CGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGGgtaattcctc ... accattacagTGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGAT

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: 46 (upstream exon), 49 (downstream exon)
Score: 67

AACGAGACACAGGTGTACGCCACCACCGCCAACTCCGGTGGCGGCAACGGCGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGGgtaattcctc ... accattacagTGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 127

AACGAGACACAGGTGTACGCCACCACCGCCAACTCCGGTGGCGGCAACGGCGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGGgtaattcctc ... accattacagTGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 77

AACGAGACACAGGTGTACGCCACCACCGCCAACTCCGGTGGCGGCAACGGCGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGGgtaattcctc ... accattacagTGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 122

AACGAGACACAGGTGTACGCCACCACCGCCAACTCCGGTGGCGGCAACGGCGTCTTCGTCGGCCTCACGCTCATCCAGTCGGCGGCGGCCAAGGGAGCGGgtaattcctc ... accattacagTGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagcagggcagtgctggtaatggttgatgcttacttcttgtgataaccattacagTGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAG
                                        tgataac  putative branch site (score: 122)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caattctggtcagaattccagtgctggaaattttagtctagcttgtagcagggcagtgctggtaatggttgatgcttacttcttgtgataaccattacagTGTGCTTGGATGGAAGCTTACCAGGTTACCACCTCCACAGAGGGTTTGGATCAGGAGCAAACAGTTGGCTCGTCAATCTCGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- -ttctggt
- - - - - - - - - - gtgctgg
- - - - - - - - - - - - - - - - - - - - - - gtagcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttgatg