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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggttcccttacagtttatactatcatgtgacttgctcctcttcattaggaacttaatatatatctgttttttttcatatgtttcctctattgactgcagGGGGAAAGAAGAGACCTATCAAATCAATAGTTGTTGGCAGGCCAATACTGCTTGCACTGGAAGATATAGATGGCAGTCCTTCTTTTCTGGAAAAAGCTTT

Basic information

species Zea mays
transcript GRMZM2G036872_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G036872_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os07g46450.1 (Oryza sativa), 3'ss of exon 6
gttggttcccttacagtttatactatcatgtgacttgctcctcttcattaggaacttaatatatatctgttttttttcatatgtttcctctattgactgcagGGGGAAAGAAGAGACCTATCAAATCAATAGTTGTTGGCAGGCCAATACTGCTTGCACTGGAAGATATAGATGGCAGTCCTTCTTTTCTGGAAAAAGCTTT
|||||||||  | |         | |  | ||||||  | || ||  | | ||| |   ||| |||||   ||||||||||  |  | ||  ||  |||||||| || ||||||| |||||||||||| | |||||||| ||||| || || ||||||||||||||||| |||||||| |||||||| || |||||||||||
gttggttcctcttc---------tctagtctgacttagttctatttgtgaagaattccctatctatct-ccttttttcatacataccatcctttctctgcagGGCGAGAGAAGAGGCCTATCAAATCATTGGTTGTTGGTAGGCCGATTCTTCTTGCACTGGAAGATATTGATGGCAGCCCTTCTTTCCTAGAAAAAGCTTT

upper sequence: GRMZM2G036872_T01 (Zea mays), 3'ss of exon 6
lower sequence: PP1S271_62V6.1 (Physcomitrella patens), 3'ss of exon 6
-gttggttcccttacagtttatactatcatgtgacttgctcctctt-cattaggaacttaatatatatctgttttttttcatatgtttcctctattgactgcagGGGGAAAGAAGAGACCTATCAAATCAATAGTTGTTGGCAGGCCAATACTGCTTGCACTGGAAGATATAGATGGCAGTCCTTCTTTTCTGGAAAAAGCTTT
           |   | |      | | |  |    | || |  ||   || |     |  |||  |||||| ||   ||  ||| ||  |   ||   | ||||  | ||   | | |   | || ||  | ||  |||||||||||||| | |||||  | |||||||| ||||| |||||||| || ||||| |||||| |
aaggaacaatttggaaatacgctgtgtaacatcgtctacttccattatcttggttgaatggtatg-atctgtattgaatcccatgattttttcttt---ttcagGAAGTAATCGGCGGCAAGTGAAGTCTCTTGTCATTGGCAGGCCAATATTACTTGCTTTAGAAGATATCGATGGAAGTCCTTCCTTCCTGGAGAAAGCTCT
















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|149074588|gb|EE162991.2|EE162991
EST:     AATATTTCGCAATGACACAACAGATGTATATGAAGGGGCTATTCCGAATT                         GGGGAAAGAAGAGACCTATCAAATCAATAGTTGTTGGCAGGCCAATACT
genomic: AATATTTCGCAATGACACAACAGATGTATATGAAGGGGCTATTCCGAATTgttggttccc ... ttgactgcagGGGGAAAGAAGAGACCTATCAAATCAATAGTTGTTGGCAGGCCAATACT
EST: gi|149074587|gb|EE162990.2|EE162990
EST:     ATATTTCGCAATGACANCAACAGATGTATATGAAGGGGCTATTCCGAATT                         GGGGAAAGAGAGAGACCTATCAAATCAATAGTTGTTGGCAGGCCAATACTG
genomic: ATATTTCGCAATGACA-CAACAGATGTATATGAAGGGGCTATTCCGAATTgttggttccc ... ttgactgcagGGGGAAAGA-AGAGACCTATCAAATCAATAGTTGTTGGCAGGCCAATACTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaggaacttaatatatatctgttttttttcatatgtttcctctattgactgcagGGGGAAAGAAGAGACCTATCAAATCAATAGTTGTTGGCAGGCCAATACTGCTTGCACTGGAAGATATAGATGGCAGTCCTTCTTTTCTGGAAAAAGCTTT
                                           tattgac  putative branch site (score: 2)
                                    tttcctctatt  CT-rich tract
     aacttaatatatatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggttcccttacagtttatactatcatgtgacttgctcctcttcattaggaacttaatatatatctgttttttttcatatgtttcctctattgactgcagGGGGAAAGAAGAGACCTATCAAATCAATAGTTGTTGGCAGGCCAATACTGCTTGCACTGGAAGATATAGATGGCAGTCCTTCTTTTCTGGAAAAAGCTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA