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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctacgtgcgcgagcgcctgccgcggtgacgtgacgaccacagatccggcggccgcgcgctagcctctgtcggtgctcatcctgctgctcgccgcgcgcagGTACCGGATGCCGGAGCGGTCGATCCCGCGGGAGGCGGCGCAGCAGATCATCAGCGACGAGCTCATGCTGGACGGCAACCCGCGCCTGAACCTGGCGTCC

Basic information

species Zea mays
transcript GRMZM2G017110_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017110_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os08g36320.2 (Oryza sativa), 3'ss of exon 1
--ctacgtgcgcgagcgcctgccgcggtgacgtgacgaccacagatccggcggccgcgcg--ctagcctctgtcggt-gctcatcctgctgctcgccgcgcgcagGTACCGGATGCCGGAGCGGTCGATCCCGCGGGAGGCGGCGCAGCAGATCATCAGCGACGAGCTCATGCTGGACGGCAACCCGCGCCTGAACCTGGCGTCC
  ||   |||  |  |   |  | ||||   ||   | |||   ||  ||  ||||||||     |      ||| | | |      | || |    | | |||||| | |||||||||||| |||||||||| ||||||||||| | |||||||||| ||||||||| ||||||||||| |||||||| |||||||||||||||
tgctggctgcatgctccgatctctcggttgggttttggcca---atttgggcgccgcgcggggctgtgctgatcgatcgattgcttcgttgttga--gtgtgcagGTTCAGGATGCCGGAGCAGTCGATCCCGAGGGAGGCGGCGTACCAGATCATCAACGACGAGCTGATGCTGGACGGGAACCCGCGGCTGAACCTGGCGTCC

upper sequence: GRMZM2G017110_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os08g36320.3 (Oryza sativa), 3'ss of exon 1
---ctacgtgcgcgagcgcctgccgcggtgacgtgacgaccacagatccggcggccgcgcgc--tagcctctgtcggt-gctcatcctgctgctcgccgcgcgcagGTACCGGATGCCGGAGCGGTCGATCCCGCGGGAGGCGGCGCAGCAGATCATCAGCGACGAGCTCATGCTGGACGGCAACCCGCGCCTGAACCTGGCGTCC
   ||   |||  |  |   |  | ||||   ||   | |||   ||  ||  ||||||||     |      ||| | | |      | || |    | | |||||| | |||||||||||| |||||||||| ||||||||||| | |||||||||| ||||||||| ||||||||||| |||||||| |||||||||||||||
gtgctggctgcatgctccgatctctcggttgggttttggcca---atttgggcgccgcgcggggctgtgctgatcgatcgattgcttcgttgttga--gtgtgcagGTTCAGGATGCCGGAGCAGTCGATCCCGAGGGAGGCGGCGTACCAGATCATCAACGACGAGCTGATGCTGGACGGGAACCCGCGGCTGAACCTGGCGTCC

upper sequence: GRMZM2G017110_T03 (Zea mays), 3'ss of exon 1
lower sequence: PP1S68_116V6.1 (Physcomitrella patens), 3'ss of exon 1
--------------ctacgtgcgcgagcgcctgccgcggtgacgtgacgacc-acagatccggcggccgcgcgctagcctctgtcggtgctcatcctgctgctcgccgcgcgcagGTACCGGATGCCGGAGCGGTCGATCCCGCGGGAGGCGGCGCAGCAGATCATCAGCGACGAGCTCATGCTGGACGGCAACCCGCGCCTGAACCTGGCGTCC
               ||| |  || |||   ||      ||  |  | |    | | ||  |||||    | ||||    || ||  || || |     | |           |||| |   || || |||||| | |  ||   ||| || ||| | |||||||||||||||||||||||| |||| |||||||| ||| ||||  ||||||||
tggagaggagaggcttacat-tgcaagcttttgttcgtttggggctatgttggatacatttggcggtattgtgctaa---ctatcactgttcttttcaatcc-----------agGTTCACCATTCCCGAGCGGGCAACACCCAAGGATGCCGCGTACCAGATCATCAGCGACGAGCTCATGTTGGATGGCAACCCTCGCTTGAATTTGGCGTCC

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|74241085|gb|DT648999.1|DT648999
EST:     CTTCGCGTCGCGCTACGTGCGCGAGCGC-CTGCCGCG                         GTACCGGATGCCGGAGCGGTCGATCCCGCGGGAGGCGGCGCAGCAGATCAT
genomic: CTTCGCGTCCCGCTACGTCCGCGA-CCCACTCCCACGgtcagtcagt ... ccgcgcgcagGTACCGGATGCCGGAGCGGTCGATCCCGCGGGAGGCGGCGCAGCAGATCAT
EST: gi|148991152|gb|EE032610.2|EE032610
EST:     CTTCGCGTCGCGCTACGTGCGCGAGCGC-CTGCCGCG                         GTACCGGATGCCGGAGCGGTCGATCCCGCGGGAGGCGGCGCAGCAGATCAT
genomic: CTTCGCGTCCCGCTACGTCCGCGA-CCCACTCCCACGgtcagtcagt ... ccgcgcgcagGTACCGGATGCCGGAGCGGTCGATCCCGCGGGAGGCGGCGCAGCAGATCAT
EST: gi|71309130|gb|DR790836.1|DR790836
EST:     GTGAGCTCCACCTTCTTCGCGTCCCGCTACGTCCGCGACCCACTCCCACG                         GTACCGGATGCCGGAGCGGTCGATCCCGCGGGAGGCGGCGCAGCAGATCAT
genomic: GTGAGCTCCACCTTCTTCGCGTCCCGCTACGTCCGCGACCCACTCCCACGgtcagtcagt ... ccgcgcgcagGTACCGGATGCCGGAGCGGTCGATCCCGCGGGAGGCGGCGCAGCAGATCAT
EST: gi|71436524|gb|DR817574.1|DR817574
EST:     CTTCGCGTCGCGCTACGTGCGCGAGCGC-CTGCCGCG                         GTACCGGATGCCGGAGCGGTCGATCCCGCGGGAGGCGGCGCAGCAGATCAT
genomic: CTTCGCGTCCCGCTACGTCCGCGA-CCCACTCCCACGgtcagtcagt ... ccgcgcgcagGTACCGGATGCCGGAGCGGTCGATCCCGCGGGAGGCGGCGCAGCAGATCAT
EST: gi|148931503|gb|EC874533.2|EC874533
EST:     CTTCGCGTCGCGCTACGTGCGCGAGCGC-CTGCCGCG                         GTACCGGATGCCGGAGCGGTCGATCCCGCGGGAGGCGGCGCAGCAGATCAT
genomic: CTTCGCGTCCCGCTACGTCCGCGA-CCCACTCCCACGgtcagtcagt ... ccgcgcgcagGTACCGGATGCCGGAGCGGTCGATCCCGCGGGAGGCGGCGCAGCAGATCAT
EST: gi|78110993|gb|DV529390.1|DV529390
EST:     CTTCGCGTCGCGCTACGTGCGCGAGCGC-CTGCCGCG                         GTACCGGATGCCGGAGCGGTCGATCCCGCGGGAGGCGGCGCAGCAGATCAT
genomic: CTTCGCGTCCCGCTACGTCCGCGA-CCCACTCCCACGgtcagtcagt ... ccgcgcgcagGTACCGGATGCCGGAGCGGTCGATCCCGCGGGAGGCGGCGCAGCAGATCAT
EST: gi|71313551|gb|DR793350.1|DR793350
EST:     CTTCGCGTCGCGCTACGTGCGCGAGCGC-CTGCCGCG                         GTACCGGATGCCGGAGCGGTCGATCCCGCGGGAGGCGGCGCAGCAGATCAT
genomic: CTTCGCGTCCCGCTACGTCCGCGA-CCCACTCCCACGgtcagtcagt ... ccgcgcgcagGTACCGGATGCCGGAGCGGTCGATCCCGCGGGAGGCGGCGCAGCAGATCAT
EST: gi|211450279|gb|FK953940.1|FK953940
EST:     GTGAGCTCCACCTTCTTCGCGTCCCGCTACGTCCGCGACCCACTCCCACG                         GTACCGGATGCC
genomic: GTGAGCTCCACCTTCTTCGCGTCCCGCTACGTCCGCGACCCACTCCCACGgtcagtcagt ... ccgcgcgcagGTACCGGATGCC
EST: gi|149088859|gb|EE177993.2|EE177993
EST:     CTTCGCGTCGCGCTACGTGCGCGAGCGC-CTGCCGCG                         GTACCGGATGCCGGAGCGGTCGATCCCGCGGGAGGCGGCGCAGCAGATCAT
genomic: CTTCGCGTCCCGCTACGTCCGCGA-CCCACTCCCACGgtcagtcagt ... ccgcgcgcagGTACCGGATGCCGGAGCGGTCGATCCCGCGGGAGGCGGCGCAGCAGATCAT
EST: gi|148973269|gb|EE024349.2|EE024349
EST:     CTTCGCGTCGCGCTACGTGCGCGAGCGC-CTGCCGCG                         GTACCGGATGCCGGAGCGGTCGATCCCGCGGGAGGCGGCGCAGCAGATCAT
genomic: CTTCGCGTCCCGCTACGTCCGCGA-CCCACTCCCACGgtcagtcagt ... ccgcgcgcagGTACCGGATGCCGGAGCGGTCGATCCCGCGGGAGGCGGCGCAGCAGATCAT
EST: gi|74242564|gb|DT650478.1|DT650478
EST:     GTGAGCTCCACCTTCTTCGCGTCCCGCTACGTCCGCGACCCACTCCCACG                         GTACCGGATGCCGGAGCGGTCGATCCCGCGGGAGGCGGCGCAGCAGATCAT
genomic: GTGAGCTCCACCTTCTTCGCGTCCCGCTACGTCCGCGACCCACTCCCACGgtcagtcagt ... ccgcgcgcagGTACCGGATGCCGGAGCGGTCGATCCCGCGGGAGGCGGCGCAGCAGATCAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctacgtgcgcgagcgcctgccgcggtgacgtgacgaccacagatccggcggccgcgcgctagcctctgtcggtgctcatcctgctgctcgccgcgcgcagGTACCGGATGCCGGAGCGGTCGATCCCGCGGGAGGCGGCGCAGCAGATCATCAGCGACGAGCTCATGCTGGACGGCAACCCGCGCCTGAACCTGGCGTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - ctgccgc
- - - - - - - - - - - - - - - - -cgaccac
- - - - - - - - - - - - - - - - - - - - - - - -gcggccg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtgctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctgctg