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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCCTCATCTAATTAGCTTCAGACCTTCTGCTCGAAATGTACCGCTGCAAGCATCAATGACTGTGACAGATGgtcagtagatatctaacttcagtttttttttaattatttgtggtttgatttgatgtcaagtttctatcatatgccaaatgttgatattcttataaaagatttttacagactctgttgcataatctttctttgtag

Basic information

species Zea mays
transcript GRMZM2G169095_T01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G169095_T01 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os06g45360.1 (Oryza sativa), 5'ss of exon 14
GTCCTCATCTAATTAGCTTCAGACCTTCTGCTCGAAATGTACCGCTGCAAGCATCAATGACTGTGACAGATGgtcagtagatatc------taacttcagttttttttta----attatttgtggtttgatttgatgtcaagtttctat-catatgccaaatgttgatattcttat--aaaagatttttacagactctg--ttgcataatctttctttgtag
|||||||||||||||||||||||||||||||| |||||||||| || |||||||| |||||||| |||||||||||||| |||||      ||||  |  ||| |||| |    | |||     |||| || |||    |  ||   || | ||   | |   | |    ||||     || |||   |  | | |     ||||| |||||||  ||| ||
GTCCTCATCTAATTAGCTTCAGACCTTCTGCTAGAAATGTACCACTACAAGCATCGATGACTGTAACAGATGgtcagtaaatatcctaaattaaccactatttattttaataggactatcaacagtttaatgtgaaactactttgtaattcttacttcgatgatagtccctcttgctgcaatgatcgatgtaaagttcaacttgcacaatcttttcttgcag

upper sequence: GRMZM2G169095_T01 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os11g33340.1 (Oryza sativa), 5'ss of exon 15
GTCCTCATCTAATTAGCTTCAGACCTTCTGCTCGAAATGTACCGCTGCAAGCATCAATGACTGTGACAGATGgtcagtagatatc-taact---tcagtttttttttaatta-------tttgtggtttgatttgatgtcaagtttctatcatatgccaaatgttgatattcttat--aaaagatttttacagactctgttgcataatctttctttgtag
||||||||| |||||||||||||||||||||| |||||||||| || |||||||| |||||||| |||||||||||||  ||||| |||||   ||| | ||| ||| | ||             |||| || |||    |  ||    ||        |||| | ||  ||||     || |||   |  | |   |    | |      | |||| ||
GTCCTCATCAAATTAGCTTCAGACCTTCTGCTAGAAATGTACCACTACAAGCATCGATGACTGTAACAGATGgtcagtgcatatcctaactggatcactatttatttcaataggactgtccaacagtttaatatgaaactactttgtagtcgaccattcaatgctaattatcttggtgcaatgatcagtgtaaaaagttcaacttgcataatatttgcag

upper sequence: GRMZM2G169095_T01 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os11g33330.1 (Oryza sativa), 5'ss of exon 16
GTCCTCATCTAATTAGCTTCAGACCTTCTGCTCGAAATGTACCGCTGCAAGCATCAATGACTGTGACAGATGgtcagtagatatctaacttcagtttttttttaattatttgtggtttgatttgatgtcaagtttctatcatatgccaaatgttgatattcttataaaagatttttacagactctgttgcataatctttctttgtag
|||||||||||||||||||||||||||||||| ||||| |||| || |||||||| |||||||| ||||| ||||||||  |  |||||   |    | |||   ||||  || |   || ||| |       ||| ||  ||  ||   | ||| |    | ||  | |     || ||      ||||| |||||||  ||| ||
GTCCTCATCTAATTAGCTTCAGACCTTCTGCTAGAAATATACCACTACAAGCATCGATGACTGTAACAGACGgtcagtattt-cctaaccgaaccactgttt--gttata-gtaggacgagttggtac-----ttcaatggtagtccg--tcttgctgcaatgatcgatg-----taaagttcaaattgcacaatcttttcttgcag

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|50323429|gb|CO518555.1|CO518555
EST:     ACCTTCTGCTCGAAATGTACCGCTGCAAGCATCAATGACTGTGACAGATG                         AGCCTGGTTATTATGAAGATGGGGCCTTTGGTATAAGATTGGAGAATGTAC
genomic: ACCTTCTGCTCGAAATGTACCGCTGCAAGCATCAATGACTGTGACAGATGgtcagtagat ... ttctttgtagAGCCTGGTTATTATGAAGATGGGGCCTTTGGTATAAGATTGGAGAATGTAC
EST: gi|60395851|gb|DN228721.1|DN228721
EST:     ACCTTCTGCTCGAAATGTACCGCTGCAAGCATCAATGACTGTGACAGATG                         AGCCTGGTTATTATGAAGATGGGGCCTTTGGTATAAGATTGGAGAATGTAC
genomic: ACCTTCTGCTCGAAATGTACCGCTGCAAGCATCAATGACTGTGACAGATGgtcagtagat ... ttctttgtagAGCCTGGTTATTATGAAGATGGGGCCTTTGGTATAAGATTGGAGAATGTAC
EST: gi|211089695|gb|FL030414.1|FL030414
EST:     ACCTTCTGCTCGAAATGTACCGCTGCAAGCATCAATGACTGTGACAGATG                         AGCCTGGTTATTATGAAGATGGGGCCTTTGGTATAAGATTGGAGAATGTAC
genomic: ACCTTCTGCTCGAAATGTACCGCTGCAAGCATCAATGACTGTGACAGATGgtcagtagat ... ttctttgtagAGCCTGGTTATTATGAAGATGGGGCCTTTGGTATAAGATTGGAGAATGTAC
EST: gi|211089690|gb|FL030409.1|FL030409
EST:     ACCTTCTGCTCGAAATGTACCGCTGCAAGCATCAATGACTGTGACAGATG                         AGCCTGGTTATTATGAAGATGGGGCCTTTGGTATAAGATTGGAGAATGTAC
genomic: ACCTTCTGCTCGAAATGTACCGCTGCAAGCATCAATGACTGTGACAGATGgtcagtagat ... ttctttgtagAGCCTGGTTATTATGAAGATGGGGCCTTTGGTATAAGATTGGAGAATGTAC
EST: gi|148948655|gb|EC898569.2|EC898569
EST:     ACCTTCTGCTCGAAATGTACCGCTGCAAGCATCAATGACTGTGACAGATG                         AGCCTGGTTATTATGAAGATGGGGCCTTTGGTATAAGATTGGAGAATGTAC
genomic: ACCTTCTGCTCGAAATGTACCGCTGCAAGCATCAATGACTGTGACAGATGgtcagtagat ... ttctttgtagAGCCTGGTTATTATGAAGATGGGGCCTTTGGTATAAGATTGGAGAATGTAC
EST: gi|71439289|gb|DR820339.1|DR820339
EST:     ACCTTCTGCTCGAAATGTACCGCTGCAAGCATCAATGACTGTGACAGATG                         AGCCTGGTTATTATGAAGATGGGGCCTTTGGTATAAGATTGGAGAATGTAC
genomic: ACCTTCTGCTCGAAATGTACCGCTGCAAGCATCAATGACTGTGACAGATGgtcagtagat ... ttctttgtagAGCCTGGTTATTATGAAGATGGGGCCTTTGGTATAAGATTGGAGAATGTAC
EST: gi|71760087|gb|DR958024.1|DR958024
EST:     ACCTTCTGCTCGAAATGTACCGCTGCAAGCATCAATGACTGTGACAGATG                         AGCCTGGTTATTATGAAGATGGGGCCTTTGGTATAAGATTGGAGAATGTAC
genomic: ACCTTCTGCTCGAAATGTACCGCTGCAAGCATCAATGACTGTGACAGATGgtcagtagat ... ttctttgtagAGCCTGGTTATTATGAAGATGGGGCCTTTGGTATAAGATTGGAGAATGTAC
EST: gi|67010801|gb|CO439550.1|CO439550
EST:     ACCTTCTGCTCGAAATGTACCGCTGCAAGCATCAATGACTGTGACAGATG                         AGCCTGGTTATTATGAAGATGGGGCCTTTGGTATAAGATTGGAGAATGTAC
genomic: ACCTTCTGCTCGAAATGTACCGCTGCAAGCATCAATGACTGTGACAGATGgtcagtagat ... ttctttgtagAGCCTGGTTATTATGAAGATGGGGCCTTTGGTATAAGATTGGAGAATGTAC
EST: gi|211089693|gb|FL030412.1|FL030412
EST:     ACCTTCTGCTCGAAATGTACCGCTTCAAGCATCAATGACTGTGACAGATG                         AGTCTGGTTATTATGAAGATGGGGCCTTTGGTATAAGATTGGAGAATGTAC
genomic: ACCTTCTGCTCGAAATGTACCGCTGCAAGCATCAATGACTGTGACAGATGgtcagtagat ... ttctttgtagAGCCTGGTTATTATGAAGATGGGGCCTTTGGTATAAGATTGGAGAATGTAC
EST: gi|211089692|gb|FL030411.1|FL030411
EST:     ACCTTCTGCTCGAAATGTACCGCTGCAAGCATCAATGACTGTGACAGATG                         AGCCTGGTTATTATGAAGATGGGGCCTTTGGTATAAGATTGGAGAATGTAC
genomic: ACCTTCTGCTCGAAATGTACCGCTGCAAGCATCAATGACTGTGACAGATGgtcagtagat ... ttctttgtagAGCCTGGTTATTATGAAGATGGGGCCTTTGGTATAAGATTGGAGAATGTAC
EST: gi|86467956|gb|DY234326.1|DY234326
EST:     ACCTTCTGCTCGAAATGTACCGCTGCAAGCATCAATGACTGTGACAGATG                         AGCCTGGTTATTATGAAGATGGGGCCTTTGGTATAAGATTGGAGAATGTAC
genomic: ACCTTCTGCTCGAAATGTACCGCTGCAAGCATCAATGACTGTGACAGATGgtcagtagat ... ttctttgtagAGCCTGGTTATTATGAAGATGGGGCCTTTGGTATAAGATTGGAGAATGTAC
EST: gi|211089696|gb|FL030415.1|FL030415
EST:     ACCTTCTGCTCGAAATGTACCGCTGCAAGCATCAATGACTGTGACAGATG                         AGCCTGGTTATTATGAAGATGGGGCCTTTGGTATAAGATTGGAGAATGTAC
genomic: ACCTTCTGCTCGAAATGTACCGCTGCAAGCATCAATGACTGTGACAGATGgtcagtagat ... ttctttgtagAGCCTGGTTATTATGAAGATGGGGCCTTTGGTATAAGATTGGAGAATGTAC
EST: gi|67018778|gb|CO447527.1|CO447527
EST:     CCTTCTGCTCGAAATGTACCGCTGNCA-GCATCAATGACTGTGACAGATG                         AGCCTGGTTATTATGAAGATGGGGCCTTTGGTATAAGATTGGAGA-TGTAC
genomic: CCTTCTGCTCGAAATGTACCGCTG-CAAGCATCAATGACTGTGACAGATGgtcagtagat ... ttctttgtagAGCCTGGTTATTATGAAGATGGGGCCTTTGGTATAAGATTGGAGAATGTAC
EST: gi|211089691|gb|FL030410.1|FL030410
EST:     ACCTTCTGCTCGAAATGTACCGCTGCAAGCATCAATGACTGTGACAGATG                         AGCCTGGTTATTATGAAGATGGGGCCTTTGGTATAAGATTGGAGAATGTAC
genomic: ACCTTCTGCTCGAAATGTACCGCTGCAAGCATCAATGACTGTGACAGATGgtcagtagat ... ttctttgtagAGCCTGGTTATTATGAAGATGGGGCCTTTGGTATAAGATTGGAGAATGTAC
EST: gi|211089694|gb|FL030413.1|FL030413
EST:     ACCTTCTGCTCGAAATGTACCGCTGCAAGCATCAATGACTGTGACAGATG                         AGCCTGGTTATTATGAAGATGGGGCCTTTGGTATAAGATTGGAGAATGTAC
genomic: ACCTTCTGCTCGAAATGTACCGCTGCAAGCATCAATGACTGTGACAGATGgtcagtagat ... ttctttgtagAGCCTGGTTATTATGAAGATGGGGCCTTTGGTATAAGATTGGAGAATGTAC
EST: gi|211092150|gb|FL030416.1|FL030416
EST:     ACCTTCTGCTCGAAATGTACCGCTGCAAGCATCAATGACTGTGACAGATG                         AGCCTGGTTATTATGAAGATGGGGCCTTTGGTATAAGATTGGAGAATGTAC
genomic: ACCTTCTGCTCGAAATGTACCGCTGCAAGCATCAATGACTGTGACAGATGgtcagtagat ... ttctttgtagAGCCTGGTTATTATGAAGATGGGGCCTTTGGTATAAGATTGGAGAATGTAC

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), 48 (downstream exon)
Score: 164

GTCCTCATCTAATTAGCTTCAGACCTTCTGCTCGAAATGTACCGCTGCAAGCATCAATGACTGTGACAGATGgtcagtagat ... ttctttgtagAGCCTGGTTATTATGAAGATGGGGCCTTTGGTATAAGATTGGAGAATGTACTTATTTGCAAAGACGCCAATGCTAAGTTTAATTTTGGAGATAAAGGTTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 338

GTCCTCATCTAATTAGCTTCAGACCTTCTGCTCGAAATGTACCGCTGCAAGCATCAATGACTGTGACAGATGgtcagtagat ... ttctttgtagAGCCTGGTTATTATGAAGATGGGGCCTTTGGTATAAGATTGGAGAATGTACTTATTTGCAAAGACGCCAATGCTAAGTTTAATTTTGGAGATAAAGGTTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 342

GTCCTCATCTAATTAGCTTCAGACCTTCTGCTCGAAATGTACCGCTGCAAGCATCAATGACTGTGACAGATGgtcagtagat ... ttctttgtagAGCCTGGTTATTATGAAGATGGGGCCTTTGGTATAAGATTGGAGAATGTACTTATTTGCAAAGACGCCAATGCTAAGTTTAATTTTGGAGATAAAGGTTA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 297

GTCCTCATCTAATTAGCTTCAGACCTTCTGCTCGAAATGTACCGCTGCAAGCATCAATGACTGTGACAGATGgtcagtagat ... ttctttgtagAGCCTGGTTATTATGAAGATGGGGCCTTTGGTATAAGATTGGAGAATGTACTTATTTGCAAAGACGCCAATGCTAAGTTTAATTTTGGAGATAAAGGTTA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCCTCATCTAATTAGCTTCAGACCTTCTGCTCGAAATGTACCGCTGCAAGCATCAATGACTGTGACAGATGgtcagtagatatctaacttcagtttttttttaattatttgtggtttgatttgatgtcaagtttctatcatatgccaaatgttgatattcttataaaagatttttacagactctgttgcataatctttctttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG