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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggccagcttcttatttttgaattttaacaaatgcataaatttctacgcattgttacttgttagccagggtactcctgatcgaatagttgctttttttgttcctcagATCCAGCTAGAGTCCTTCAACCCTGACTCTTCATCAACAGCATCCAGAATAACATGCTCTGATGACAGATGTACAGCTGGCTTCCAAACAGGGGAAGCAA

Basic information

species Zea mays
transcript GRMZM2G133029_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G133029_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g56930.2 (Oryza sativa), 3'ss of exon 2
-------------------gtgaggccagcttcttatttttga-attttaacaaatgcataa--atttctacgcattg--ttacttgttagccagggtac-tcctgatcgaatagttgctttttttgttcctcagATCCAGCTAGAGTCCTTCAACCCTGACTCTTCATCAACAGCATCCAGAATAACATGCTCTGATGACAGATGTACAGCTGGCTTCCAAACAGGGGAAGCAA
                   | |     | | |  | | | ||| ||    ||||  ||||    ||  ||    || |  |||| | | ||    | | | | ||||| | ||  || |||| | ||||  |||||||||| | |||| |||||| |||||| ||||||||||| |||||| |||| ||||||| ||||| || |||||||||| | | |||||| | |||||| 
gtgagacatctcattctttgcgctcttatccttatctctatgacatgcatacaacagcattgttatcccttgagatggacttacctatcagttgagattcattctgattggattattactttatatgtttttcagATCCAGTTGGAGTTCTTCAATCCTGACACTTCATCAACATCATCCAAAATACCATGCTCAGATGATAGGTGTACAGCTGCCCTTCAAACAAGCGAAGCAG
















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|149087990|gb|EE177209.2|EE177209
EST:     GGGTCACTTGCAGTCCTTGCACTGGTTGCCCGACATCAAGTGGACTCAAT                         ATCCAGCTAGAGTCCTTCAACCCTGACTCTTCATCAACAGCATCCAGAATA
genomic: GGGTCACTTGCAGTCCTTGCACTGGTTGCCCGACATCAAGTGGACTCAATgtgaggccag ... tgttcctcagATCCAGCTAGAGTCCTTCAACCCTGACTCTTCATCAACAGCATCCAGAATA
EST: gi|19058043|gb|BM736710.1|BM736710
EST:     AGTCCTTGCACTGGTTGCCCGACATCAAGTGGACTCAAT                         ATCCAGCTAGAGTCCTTCAACCCTGACTCTTCATCAACAGCATCCAGAATA
genomic: AGTCCTTGCACTGGTTGCCCGACATCAAGTGGACTCAATgtgaggccag ... tgttcctcagATCCAGCTAGAGTCCTTCAACCCTGACTCTTCATCAACAGCATCCAGAATA
EST: gi|110539477|gb|EE043397.1|EE043397
EST:     GGGTCACTTGCAGTCCTTGCACTGGTTGCCCGACATCAAGTGGACTCAAT                         ATCCAGCTAGAGTCCTTCAACCCTGACTCTTCATCAACAGCATCCAGAATA
genomic: GGGTCACTTGCAGTCCTTGCACTGGTTGCCCGACATCAAGTGGACTCAATgtgaggccag ... tgttcctcagATCCAGCTAGAGTCCTTCAACCCTGACTCTTCATCAACAGCATCCAGAATA
EST: gi|87153408|gb|DY398197.1|DY398197
EST:     GGGTCACTTGCAGTCCTTGCACTGGTTGCCCGACATCAAGTGGACTCAAT                         ATCCAGCTAGAGTCCTTCAACCCTGACTCTTCATCAACAGCATCCAGAATA
genomic: GGGTCACTTGCAGTCCTTGCACTGGTTGCCCGACATCAAGTGGACTCAATgtgaggccag ... tgttcctcagATCCAGCTAGAGTCCTTCAACCCTGACTCTTCATCAACAGCATCCAGAATA
EST: gi|19436559|gb|BM952969.1|BM952969
EST:     GGGTCACTTGCAGTCCTTGCACTGGTTGCCCGACATCAAGTGGACTCAAT                         ATCCAGCTAGAGTCCTTCAACCCTGACTCTTCATCAACAGCATCCAGAATA
genomic: GGGTCACTTGCAGTCCTTGCACTGGTTGCCCGACATCAAGTGGACTCAATgtgaggccag ... tgttcctcagATCCAGCTAGAGTCCTTCAACCCTGACTCTTCATCAACAGCATCCAGAATA
EST: gi|149096290|gb|EE182005.2|EE182005
EST:     GGGTCACTTGCAGTCCTTGCACTGGTTGCCCGACATCAAGTGGACTCAAT                         ATCCAGCTAGAGTCCTTCAACCCTGACTCTTCATCAACAGCATCCAGAATA
genomic: GGGTCACTTGCAGTCCTTGCACTGGTTGCCCGACATCAAGTGGACTCAATgtgaggccag ... tgttcctcagATCCAGCTAGAGTCCTTCAACCCTGACTCTTCATCAACAGCATCCAGAATA
EST: gi|22491523|gb|BU051446.1|BU051446
EST:     GGGTCACTTGCAGTCCTTGCACTGGTTGCCCGACATCAAGTGGACTCAAT                         ATCCAGCTAGAGTCCTTCAACCCTGACTCTTCATCAACAGCATCCAGAATA
genomic: GGGTCACTTGCAGTCCTTGCACTGGTTGCCCGACATCAAGTGGACTCAATgtgaggccag ... tgttcctcagATCCAGCTAGAGTCCTTCAACCCTGACTCTTCATCAACAGCATCCAGAATA
EST: gi|148983003|gb|EE028898.2|EE028898
EST:     GGGTCACTTGCAGTCCTTGCACTGGTTGCCCGACATCAAGTGGACTCAAT                         ATCCAGCTAGAGTCCTTCAACCCTGACTCTTCATCAACAGCATCCAGAATA
genomic: GGGTCACTTGCAGTCCTTGCACTGGTTGCCCGACATCAAGTGGACTCAATgtgaggccag ... tgttcctcagATCCAGCTAGAGTCCTTCAACCCTGACTCTTCATCAACAGCATCCAGAATA
EST: gi|149044646|gb|EE047618.2|EE047618
EST:     GGGTCACTTGCAGTCCTTGCACTGGTTGCCCGACATCAAGTGGACTCAAT                         ATCCAGCTAGAGTCCTTCAACCCTGACTC-TCATCAACAGCATCCAGAATA
genomic: GGGTCACTTGCAGTCCTTGCACTGGTTGCCCGACATCAAGTGGACTCAATgtgaggccag ... tgttcctcagATCCAGCTAGAGTCCTTCAACCCTGACTCTTCATCAACAGCATCCAGAATA
EST: gi|148940293|gb|EC885075.2|EC885075
EST:     GGGTCACTTGCAGTCCTTGCACTGGTTGCCCGACATCAAGTGGACTCAAT                         ATCCAGCTAGAGTCCTTCAACCCTGACTCTTCATCAACAGCATCCAGAATA
genomic: GGGTCACTTGCAGTCCTTGCACTGGTTGCCCGACATCAAGTGGACTCAATgtgaggccag ... tgttcctcagATCCAGCTAGAGTCCTTCAACCCTGACTCTTCATCAACAGCATCCAGAATA
EST: gi|60339993|gb|DN206966.1|DN206966
EST:     GGGTCACTTGCAGTCCTTGCACTGGTTGCCCGACATCAAGTGGACTCAAT                         ATCCAGCTAGAGTCCTTCAACCCTGACTCTTCATCAACAGCATCCAGAATA
genomic: GGGTCACTTGCAGTCCTTGCACTGGTTGCCCGACATCAAGTGGACTCAATgtgaggccag ... tgttcctcagATCCAGCTAGAGTCCTTCAACCCTGACTCTTCATCAACAGCATCCAGAATA
EST: gi|19436231|gb|BM952641.1|BM952641
EST:     GGGTCAC-TGCAGTCCTTGCACTGGTTGCCCGACATCAAGTGGACTCAAT                         ATCCAGCTAGAGTCCTTCAACCCTGACTCTTCATCAACAGCATCCAGAATA
genomic: GGGTCACTTGCAGTCCTTGCACTGGTTGCCCGACATCAAGTGGACTCAATgtgaggccag ... tgttcctcagATCCAGCTAGAGTCCTTCAACCCTGACTCTTCATCAACAGCATCCAGAATA
EST: gi|19351139|gb|BM895671.1|BM895671
EST:     GGGTCACTTGCAGTCCNTGCACTGGTTGCCCGACATCAAGTGGACTCAAT                         ATCCAGCTAGAGTCCTTCAACCCTGACTCTTCATCAACAGCATCCAGAATA
genomic: GGGTCACTTGCAGTCCTTGCACTGGTTGCCCGACATCAAGTGGACTCAATgtgaggccag ... tgttcctcagATCCAGCTAGAGTCCTTCAACCCTGACTCTTCATCAACAGCATCCAGAATA
EST: gi|148966491|gb|EE017508.2|EE017508
EST:     GGGTCACTTGCAGTCCTTGCACTGGTTGCCCGACATCAAGTGGACTCAAT                         ATCCAGCTAGAGTCCTTCAACCCTGACTCTTCATCAACAGCATCCAGAATA
genomic: GGGTCACTTGCAGTCCTTGCACTGGTTGCCCGACATCAAGTGGACTCAATgtgaggccag ... tgttcctcagATCCAGCTAGAGTCCTTCAACCCTGACTCTTCATCAACAGCATCCAGAATA
EST: gi|148961307|gb|EE012032.2|EE012032
EST:     GGGTCACTTGCAGTCCTTGCACTGGTTGCCCGACATCAAGTGGACTCAAT                         ATCCAGCTAGAGTCCTTCAACCCTGACTCTTCATCAACAGCATCCAGAATA
genomic: GGGTCACTTGCAGTCCTTGCACTGGTTGCCCGACATCAAGTGGACTCAATgtgaggccag ... tgttcctcagATCCAGCTAGAGTCCTTCAACCCTGACTCTTCATCAACAGCATCCAGAATA
EST: gi|149108251|gb|EE292593.2|EE292593
EST:     GGGTCACTTGCAGTCCTTGCACTGGTTGCCCGACATCAAGTGGACTCAAT                         ATCCAGCTAGAGTCCTTCAACCCTGACTCTTCATCAACAGCATCCAGAATA
genomic: GGGTCACTTGCAGTCCTTGCACTGGTTGCCCGACATCAAGTGGACTCAATgtgaggccag ... tgttcctcagATCCAGCTAGAGTCCTTCAACCCTGACTCTTCATCAACAGCATCCAGAATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttacttgttagccagggtactcctgatcgaatagttgctttttttgttcctcagATCCAGCTAGAGTCCTTCAACCCTGACTCTTCATCAACAGCATCCAGAATAACATGCTCTGATGACAGATGTACAGCTGGCTTCCAAACAGGGGAAGCAA
                     tcctgat  putative branch site (score: 3)
                                   ttgctttttttgttcc  putative PPT
                                       tttttttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaggccagcttcttatttttgaattttaacaaatgcataaatttctacgcattgttacttgttagccagggtactcctgatcgaatagttgctttttttgttcctcagATCCAGCTAGAGTCCTTCAACCCTGACTCTTCATCAACAGCATCCAGAATAACATGCTCTGATGACAGATGTACAGCTGGCTTCCAAACAGGGGAAGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA