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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcttaagaaaacttattcttgaaatacttaactaagactacaaggacccagttattcatgacacctctcatgtttctcacacataattaagtaatagaaaaaaactggactattaacggatttcaggctggtcgctggctgagctcttgctccttgtttacagCATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATTGACAAAGATGGCAAGATAAGCCTAGATGAATTTCGCCGGCTCTTGAAGA

Basic information

species Zea mays
transcript GRMZM2G365035_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G365035_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g22710.4 (Oryza sativa), 3'ss of exon 8
--gtatcttaagaaaacttattcttgaaatacttaactaagactacaaggacccagttattcatg-acacctctcatgtttctcacacataattaagtaatagaaaaaaactgga--ctattaacggatttcaggctggtcgctggctgagctcttgctccttgtttacagCATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATTGACAAAGATGGCAAGATAAGCCTAGATGAATTTCGCCGGCTCTTGAAGA
    | ||    |||   ||    ||||| | |   ||    |||     ||      ||| ||  |   |    | | |||  |  | |||||     |||| | || |  | |   |||| |   | |||| |||  ||  |   ||   |||| |   |||| | ||||| |||||| |||| |||||||||||||||||||||||||||||||||||||||| |||||| || ||||||||||||||||||||| ||||| |||| |
gtacacctcttcaaa---tacctgtgaaacattactcttttcctattc--acgtgagaattgatttatttcctataagattccaatccttaattggtgcatagcataagatcgtaatttattcaaccagttcatgcttctca-tatatgtattcttaca--ttgtctgcagCAAACAGGACTGAAAGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATTGACAGAGATGGAAAAATAAGCCTAGATGAATTTCGCAGGCTCCTGAAAA
















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|18649798|gb|BM498617.1|BM498617
EST:     AGAGATGGCTACATCACACCTGATGAACTTAGAATG                         CATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
genomic: AGAGATGGCTACATCACACCTGATGAACTTAGAATGgtatcttaag ... ttgtttacagCATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
EST: gi|60338755|gb|DN205728.1|DN205728
EST:     AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATG                         CATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
genomic: AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATGgtatcttaag ... ttgtttacagCATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
EST: gi|4688566|gb|AI637236.1|AI637236
EST:     AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATG                         CATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACANT
genomic: AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATGgtatcttaag ... ttgtttacagCATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
EST: gi|61118774|gb|DN559735.1|DN559735
EST:     AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATG                         CATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
genomic: AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATGgtatcttaag ... ttgtttacagCATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
EST: gi|166632170|gb|EG309972.1|EG309972
EST:     CTACATCACACCTGATGAACTTAGAATG                         CATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
genomic: CTACATCACACCTGATGAACTTAGAATGgtatcttaag ... ttgtttacagCATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
EST: gi|18384244|gb|BM417443.1|BM417443
EST:     AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATG                         CATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
genomic: AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATGgtatcttaag ... ttgtttacagCATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
EST: gi|113701806|gb|EE679310.1|EE679310
EST:     AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATG                         CATACAGGAATGAAGGGTTTTATTGATCCCCTCCTGGAGGAGGCTGACATT
genomic: AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATGgtatcttaag ... ttgtttacagCATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
EST: gi|12058142|gb|BF727762.2|BF727762
EST:     AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATG                         CATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
genomic: AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATGgtatcttaag ... ttgtttacagCATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
EST: gi|6696017|gb|AW289125.1|AW289125
EST:     AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATG                         CATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT
genomic: AATTTGATGTTGACAGAGATGGCTACATCACACCTGATGAACTTAGAATGgtatcttaag ... ttgtttacagCATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actattaacggatttcaggctggtcgctggctgagctcttgctccttgtttacagCATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATTGACAAAGATGGCAAGATAAGCCTAGATGAATTTCGCCGGCTCTTGAAGA
  tattaac  putative branch site (score: 1)
                                   ctcttgctccttgttt  putative PPT
                                             ttgttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcttaagaaaacttattcttgaaatacttaactaagactacaaggacccagttattcatgacacctctcatgtttctcacacataattaagtaatagaaaaaaactggactattaacggatttcaggctggtcgctggctgagctcttgctccttgtttacagCATACAGGAATGAAGGGTTCTATTGATCCCCTCCTGGAGGAGGCTGACATTGACAAAGATGGCAAGATAAGCCTAGATGAATTTCGCCGGCTCTTGAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA