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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAGCAATGTTCCTTGCACAAGCCATGTTGTGGGATCAAATTACTGCTTCATGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgccttcagtcaactttatcccacataagtatgcatcaaaaataatatcacataattaagatgcacatagaccttacaagctatgtttcaacattgcag

Basic information

species Zea mays
transcript GRMZM2G038848_T01
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G038848_T02 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os03g42110.1 (Oryza sativa), 5'ss of exon 13
TAGCAATGTTCCTTGCACAAGCCATGTTGTGGGATCAAATTACTGCTTCATGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgccttcagtcaactttatcccacataagtatgcatcaaaaataatatcacataattaagatgcacatagaccttacaagctatgtttcaacattgcag
|||||  ||||||  |||| ||||||||||||||||||||||||||||||||||||||| |||||| ||||| |||||| | ||||||||||| ||||| ||||||| |||   ||| ||  ||    |  ||| ||  | |||   |||| ||| | | || ||||||| |   | | ||     | | |||||||| |||||
TAGCAGCGTTCCTCACACACGCCATGTTGTGGGATCAAATTACTGCTTCATGAATGTCTTTGAGGACAGAATTCCTGGACGTGCCATCATCATATCTGTTgtaagtgtctt---tcatctacatgtttctcaagcatttagcaatc-taatgtcatagacttcagatgcata---atcctatttcttgt-tttcaacaatgcag

upper sequence: GRMZM2G038848_T02 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os10g35170.1 (Oryza sativa), 5'ss of exon 13
TAGCAATGTTCCTTGCACAAGCCATGTTGTGGGATCAAATTACTGCTTCATGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgccttcagtcaactttatcccacataagtatgcatcaaaaataatatcacataattaagatgcacatagaccttacaagct-atgtttcaacattgcag
 |||| |||||||  |||  ||||||| |||||||||||||||||||||||||||||||  ||||| || || |||||||||||||||||||||||||| ||| | | |||||  || |||||| || |||         |||||  || | ||     | | | |    |  |   ||||    ||  |  ||||||    |||
CAGCACTGTTCCTCACACGCGCCATGTCGTGGGATCAAATTACTGCTTCATGAATGTCTTCGAGGACAGGATTCCTGGAAGGGCCATCATCATCTCTGTTgtatgcgtcttcaaccatctttatgcc-cat-------tgtcaaac-tagtttcttcagacttaaagatgcgaaattcttattttcttgttcttcaactccacag

upper sequence: GRMZM2G038848_T02 (Zea mays), 5'ss of exon 13
lower sequence: PP1S101_184V6.1 (Physcomitrella patens), 5'ss of exon 12
TAGCAATGTTCCTTGCACAAGCCATGTTGTGGGATCAAATTACTGCTTCATGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgccttcagtcaactttatcccacataagtatgcatcaaaaataatatcacataattaagatgcacatagaccttacaagctatgtttcaacattgcag
  | |  |  |||   ||| |||| ||   ||||||||| || ||||| |||||||| | ||||||| | || |||||||| || |||||||||||||| |||||  |  |||     |    ||| |   || ||       |    || | ||      |    ||    |   | |   || | | |  | |   | |   
GGGTATAGCACCTCATACACGCCACGTACGGGGATCAAACTATTGCTTGATGAATGTTTTTGAGGATCGGATTCCTGGAAGAGCAATCATCATCTCTGTGgtaag--ctctcaacacgcacgttccaatggaaataatttcttatgtgaacaccatcactatgccctgagttttttcttctgaaaccacggattagt-tagtt-

upper sequence: GRMZM2G038848_T02 (Zea mays), 5'ss of exon 13
lower sequence: EFJ17635 (Selaginella moellendorffii), 5'ss of exon 11
TAGCAATGTTCCTTGCACAAGCCATGTTGTGGGATCAAATTACTGCTTCATGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgccttcagtcaactttatcccacataagtatgcatcaaaaataatatcacataattaagatgcacatagaccttacaagctatgtttcaacattgcag
  | |  || ||   |||  |||| | |   |||||||| ||||||||||| ||||||| ||| || || ||  ||| ||| || |||||||||||||| ||||||         |||    |||  || |      | |  ||||| | | ||   |  |   |                                       
GGGAATCGTCCCACACACTCGCCACGCTCGAGGATCAAACTACTGCTTCATCAATGTCTTTGAAGACAGGATCTCTGCAAGAGCTATCATCATCTCTGTGgtaagt--------ccaaacacatct-acgtggaatggaagaaaaaacactttccttttctcttggcag-----------------------------------

upper sequence: GRMZM2G038848_T02 (Zea mays), 5'ss of exon 13
lower sequence: EFJ29102 (Selaginella moellendorffii), 5'ss of exon 11
TAGCAATGTTCCTTGCACAAGCCATGTTGTGGGATCAAATTACTGCTTCATGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgccttcagtcaactttatcccacataagtatgcatcaaaaataatatcacataattaagatgcacatagaccttacaagctatgtttcaacattgcag
  | |  || ||   |||  |||| | |   |||||||| ||||||||||| ||||||| ||| || || ||  ||| ||| || |||||||||||||| ||||||     ||  ||  | ||      || |      |  ||||| | | ||   |      |                                       
GGGAATCGTCCCACACACTCGCCACGCTCGAGGATCAAACTACTGCTTCATCAATGTCTTTGAAGACAGGATCTCTGCAAGAGCTATCATCATCTCTGTGgtaagt----ccaaacacatctacgtggaatgaa-----agaaaaaacactttccttttcgcttggcag-----------------------------------

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|30705886|gb|CD058958.1|CD058958
EST:     TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTC                         ATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
genomic: TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
EST: gi|37397485|gb|CF636042.1|CF636042
EST:     TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTC                         ATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
genomic: TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
EST: gi|6448353|gb|AW181119.1|AW181119
EST:     TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTC                         ATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
genomic: TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
EST: gi|88747566|gb|DY531707.1|DY531707
EST:     TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATTTCTGTC                         ATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
genomic: TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
EST: gi|32931445|gb|CF036257.1|CF036257
EST:     TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTC                         ATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
genomic: TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
EST: gi|110202395|gb|EC884292.1|EC884292
EST:     TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTC                         ATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
genomic: TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
EST: gi|32912849|gb|CF017661.1|CF017661
EST:     GGGCCATCATCATCTCTGTC                         ATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
genomic: GGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
EST: gi|32930019|gb|CF034831.1|CF034831
EST:     TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTC                         ATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
genomic: TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
EST: gi|71762552|gb|DR960489.1|DR960489
EST:     TGAATGTTTATGAGGATAGAATACCTGGAAGGGCCATCATCATTTCTGTC                         ATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATTTTAAT
genomic: TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
EST: gi|148958090|gb|EC904281.2|EC904281
EST:     TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTC                         ATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
genomic: TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
EST: gi|74234670|gb|DT642584.1|DT642584
EST:     TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTC                         ATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
genomic: TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
EST: gi|60394782|gb|DN227652.1|DN227652
EST:     TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTC                         ATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
genomic: TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
EST: gi|87155331|gb|DY400120.1|DY400120
EST:     TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTC                         ATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
genomic: TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
EST: gi|26558690|gb|CA830925.1|CA830925
EST:     TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTC                         ATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
genomic: TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
EST: gi|33093061|gb|CF053055.1|CF053055
EST:     TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTC                         ATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
genomic: TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
EST: gi|60337236|gb|DN204209.1|DN204209
EST:     TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTC                         ATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
genomic: TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
EST: gi|148942778|gb|EC887805.2|EC887805
EST:     TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTC                         ATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
genomic: TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
EST: gi|19437017|gb|BM953427.1|BM953427
EST:     TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTC                         ATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
genomic: TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
EST: gi|32931562|gb|CF036374.1|CF036374
EST:     TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTC                         ATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
genomic: TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
EST: gi|40337039|gb|CK371109.1|CK371109
EST:     TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTC                         ATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
genomic: TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
EST: gi|78080159|gb|DV508571.1|DV508571
EST:     TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATTTTTGTC                         ATAGATAATTTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
genomic: TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
EST: gi|22473066|gb|BU037546.1|BU037546
EST:     TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTC                         ATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
genomic: TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
EST: gi|5706123|gb|AI941899.1|AI941899
EST:     TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTC                         ATAGATAATCTTGTGAAG
genomic: TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAG
EST: gi|211026572|gb|FL468584.1|FL468584
EST:     TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTC                         ATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
genomic: TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
EST: gi|78079273|gb|DV507685.1|DV507685
EST:     TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTC                         ATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
genomic: TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
EST: gi|148943027|gb|EC888077.2|EC888077
EST:     TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATTTCTGTC                         ATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
genomic: TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
EST: gi|67010559|gb|CO439308.1|CO439308
EST:     GAATGTCTATGAGGATAGAATACCTGGANAGG-CCATCATCATCTCTGTC                         ATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
genomic: GAATGTCTATGAGGATAGAATACCTGGA-AGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAGCAATGTTCCTTGCACAAGCCATGTTGTGGGATCAAATTACTGCTTCATGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgccttcagtcaactttatcccacataagtatgcatcaaaaataatatcacataattaagatgcacatagaccttacaagctatgtttcaacattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG