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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttctcatgtagccttttgactaacatacaatttgtttattacacctggtaaatcctttatctatcagatattatgtgcttttttatgattcttttcagGCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG

Basic information

species Zea mays
transcript GRMZM2G094978_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G094978_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g36750.1 (Oryza sativa), 3'ss of exon 5
---ttttctcatgtagccttttgactaacatacaatttgtt--tattacacctggtaaatcctttatctatcagatattatgtgcttttttatgattcttttcagGCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG
   ||| || ||||||    |  | |||| |    | || |   |||  |       | | | ||    |  ||| | |||||   |||||||    |||| |||||||||||| || | |||||||| ||||||||||| ||||||   ||
atatttgcttatgtaggaagt-aattaacttttcttgtgctataattggattcctggatttcatttctcacgagagagtatgtttctttttat----ctttgcagGCAATCTACTTACTTGCAGCAACCACACTTGGAGTCGATCCATCTAG
















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|211136606|gb|FL156037.1|FL156037
EST:     AGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCA                         GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG
genomic: AGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCAgtaagttgat ... ttcttttcagGCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG
EST: gi|91056651|gb|EB167069.1|EB167069
EST:     AGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCA                         GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG
genomic: AGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCAgtaagttgat ... ttcttttcagGCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG
EST: gi|149014075|gb|EE043602.2|EE043602
EST:     AGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCA                         GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAGCTGT
genomic: AGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCAgtaagttgat ... ttcttttcagGCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAGCTGT
EST: gi|88753379|gb|DY537520.1|DY537520
EST:     AGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCA                         GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG
genomic: AGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCAgtaagttgat ... ttcttttcagGCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG
EST: gi|86467368|gb|DY233738.1|DY233738
EST:     AGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCA                         GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG
genomic: AGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCAgtaagttgat ... ttcttttcagGCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG
EST: gi|149112364|gb|EE295251.2|EE295251
EST:     AGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCA                         GGCA-TCTACATA
genomic: AGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCAgtaagttgat ... ttcttttcagG-CAATCTACATA
EST: gi|86470646|gb|DY237016.1|DY237016
EST:     TTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCA                         GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG
genomic: TTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCAgtaagttgat ... ttcttttcagGCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG
EST: gi|13558959|gb|BG550314.1|BG550314
EST:     CAAAAAGCCTGACCCA                         GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG
genomic: CAAAAAACCTGACCCAgtaagttgat ... ttcttttcagGCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG
EST: gi|211329033|gb|FL456230.1|FL456230
EST:     AGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCA                         GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG
genomic: AGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCAgtaagttgat ... ttcttttcagGCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG
EST: gi|50333792|gb|CO528918.1|CO528918
EST:     AGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCA                         GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAGCT
genomic: AGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCAgtaagttgat ... ttcttttcagGCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAGCT
EST: gi|71764323|gb|DR962260.1|DR962260
EST:     AGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCA                         GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG
genomic: AGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCAgtaagttgat ... ttcttttcagGCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG
EST: gi|101388001|gb|EB816015.1|EB816015
EST:     CAAAAAACCTGACCCA                         GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG
genomic: CAAAAAACCTGACCCAgtaagttgat ... ttcttttcagGCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG
EST: gi|93011639|gb|EB637159.1|EB637159
EST:     AGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCA                         GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG
genomic: AGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCAgtaagttgat ... ttcttttcagGCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG
EST: gi|71300514|gb|DR786312.1|DR786312
EST:     AGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCA                         GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG
genomic: AGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCAgtaagttgat ... ttcttttcagGCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG
EST: gi|60352425|gb|DN219398.1|DN219398
EST:     AGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCA                         GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG
genomic: AGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCAgtaagttgat ... ttcttttcagGCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG
EST: gi|71766391|gb|DR964328.1|DR964328
EST:     AGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCA                         GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG
genomic: AGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCAgtaagttgat ... ttcttttcagGCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG
EST: gi|101382873|gb|EB813490.1|EB813490
EST:     AGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCA                         GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG
genomic: AGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCAgtaagttgat ... ttcttttcagGCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG
EST: gi|60357150|gb|DN224123.1|DN224123
EST:     AGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCA                         GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG
genomic: AGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCAgtaagttgat ... ttcttttcagGCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG
EST: gi|71448345|gb|DR829395.1|DR829395
EST:     AGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCA                         GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG
genomic: AGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCAgtaagttgat ... ttcttttcagGCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG
EST: gi|71300530|gb|DR786320.1|DR786320
EST:     AGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCA                         GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG
genomic: AGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCAgtaagttgat ... ttcttttcagGCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG
EST: gi|50327117|gb|CO522243.1|CO522243
EST:     AGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCA                         GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG
genomic: AGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCAgtaagttgat ... ttcttttcagGCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG
EST: gi|101388003|gb|EB816016.1|EB816016
EST:     AGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCA                         GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG
genomic: AGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCAgtaagttgat ... ttcttttcagGCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG
EST: gi|71766392|gb|DR964329.1|DR964329
EST:     AGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCA                         GCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG
genomic: AGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCAgtaagttgat ... ttcttttcagGCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG

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), 43 (downstream exon)
Score: 62

GTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCAgtaagttgat ... ttcttttcagGCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 537

GTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCAgtaagttgat ... ttcttttcagGCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG


Block sizes: 45 (upstream exon), 36 (downstream exon)
Score: 8

GTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCAgtaagttgat ... ttcttttcagGCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 145

GTTTCAGCAATAGTGTCGTACTTATTGGGGCCTGATAGAGCTGATAAGATTACCATATTTGCTGGAGATGTGGTTCCTCACAAAAAACCTGACCCAgtaagttgat ... ttcttttcagGCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctggtaaatcctttatctatcagatattatgtgcttttttatgattcttttcagGCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG
                                             ttcttttc  CT-rich tract
                                   ttttttatgattcttt  TA-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttctcatgtagccttttgactaacatacaatttgtttattacacctggtaaatcctttatctatcagatattatgtgcttttttatgattcttttcagGCAATCTACATATTAGCAGCAACTACACTTGGAGTTGATCCACAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG