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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcataatcgatttcttttcttctccacattttcgagaaagtatttcttttttgaatttttctaatagtagttgttctgcagGCGATTGCTACCGAGGTGCAAAGTGAGTCCAAGTGGAAGATATTAGGGGAGTTAGCTATGTCAAGTGGAAAG

Basic information

species Zea mays
transcript GRMZM2G141587_T02
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G141587_T02 (Zea mays), 3'ss of exon 18
lower sequence: LOC_Os02g11840.1 (Oryza sativa), 3'ss of exon 9
gcataatcgatttcttttcttctccacattttcgagaaagtattt--cttttttgaatttttctaatagtagttgttctgcagGCGATTGCTACCGAGGTGCAAAGTGAGTCCAAGTGGAAGATATTAGGGGAGTTAGCTATGTCAAGTGGAAAG
||| |   ||||  |||  || || |||||| | |||| || |||  |||| || || | || | | | || ||| | | ||||| ||||| |  ||||  ||||||||||||||||||| |   ||||| ||||||||||||||||  ||||||
gcacagatgattaatttatttatc-acatttccaagaatgtttttgtctttgttcaaatgttgtta-actatttgcttttcagGCAATTGCCATTGAGGCACAAAGTGAGTCCAAGTGGAGGCAGTTAGGAGAGTTAGCTATGTCAACCGGAAAG

upper sequence: GRMZM2G141587_T02 (Zea mays), 3'ss of exon 18
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 18
-----------------------------------------------------------------gcataatcgatttcttttcttctccacattttcgagaaagtatttcttttt--tgaatttttctaa----tagta-gttgttctg------cagGCGATTGCTACCGAGGTGCAAAGTGAGTCCAAGTGGAAGATATTAGGGGAGTTAGCTATGTCAAGTGGAAAG
                                                                 | | | |  |   | | | |  |      |   ||   | || | || | |    | ||| ||| |    ||| | | | ||||       ||||  |||||||| || |||||||||||||| || ||||||  ||| || || ||||||||||| | |||||||
gtaaattatgttgattttatgtcagtatagggatataaactagttctttgacagtttgttgacttgaacatttaagcacatctttattttcttctgaggaatgattagtcctctgtgacaattttatctgaaatatagcatgatcttctttgctttcagGACATTGCTACAGAAGTGCAAAGTGAGTCAAAATGGAAGCAATTGGGAGAATTAGCTATGTCCACTGGAAAG
















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|18384334|gb|BM417533.1|BM417533
EST:     ATTACAGATTTGACCTGGCTGTGCAACTTGGTCGACTTGAAATTGCGAAG                         GCGATTGCTACCGAGGTGCAAAGTGAGTCCAAGTGGAAGATATTAGGGGAG
genomic: ATTACAGATTTGACCTGGCTGTGCAACTTGGTCGACTTGAAATTGCGAAGgcataatcga ... tgttctgcagGCGATTGCTACCGAGGTGCAAAGTGAGTCCAAGTGGAAGATATTAGGGGAG
EST: gi|18384433|gb|BM417632.1|BM417632
EST:     ATTACAGATTTGACCTGGCTGTGCAACTTGGTCGACTTGAAATTGCGAAG                         GCGATTGC-ACC-AGGTGCAA-GTGAGTCCA-GTGGAAGATATTAGGGGAG
genomic: ATTACAGATTTGACCTGGCTGTGCAACTTGGTCGACTTGAAATTGCGAAGgcataatcga ... tgttctgcagGCGATTGCTACCGAGGTGCAAAGTGAGTCCAAGTGGAAGATATTAGGGGAG
EST: gi|211291668|gb|FL235608.1|FL235608
EST:     ATTACAGATTTGACCTGGCTGTGCAACTTGGTCGACTTGAAATTGCAAAG                         GCGATTGCTACCGAGGTGCAAAGTGAGTCCAAGTGGAAGATATTAGGGGAG
genomic: ATTACAGATTTGACCTGGCTGTGCAACTTGGTCGACTTGAAATTGCGAAGgcataatcga ... tgttctgcagGCGATTGCTACCGAGGTGCAAAGTGAGTCCAAGTGGAAGATATTAGGGGAG
EST: gi|22489660|gb|BU049570.1|BU049570
EST:     ATTACAGATTTGACCTGGCTGTGCAACTTGGTCGACTTGAAATTGCGAAG                         GCGATTGCTACCGAGGTGCAAAGTGAGTCCA-GTGGAAGATA
genomic: ATTACAGATTTGACCTGGCTGTGCAACTTGGTCGACTTGAAATTGCGAAGgcataatcga ... tgttctgcagGCGATTGCTACCGAGGTGCAAAGTGAGTCCAAGTGGAAGATA
EST: gi|18649807|gb|BM498626.1|BM498626
EST:     ATTACAGATTTGACCTGGCTGTGCAACTTGGTCGACTTGAAATTGCGAAG                         GCGATTGCTACCGAGGTGCAAAGTGAGTCCAAGTGGAAGATATTAGGGGAG
genomic: ATTACAGATTTGACCTGGCTGTGCAACTTGGTCGACTTGAAATTGCGAAGgcataatcga ... tgttctgcagGCGATTGCTACCGAGGTGCAAAGTGAGTCCAAGTGGAAGATATTAGGGGAG
EST: gi|56382379|gb|CV985048.1|CV985048
EST:     ATTACAGATTTGACCTGGCTGTGCAACTTGGTCGACTTGAAATTGCAAAG                         GCGATTGCTACCGAGGTGCAAAGTGAGTCCAAGTGGAAGATATTAGGGGAG
genomic: ATTACAGATTTGACCTGGCTGTGCAACTTGGTCGACTTGAAATTGCGAAGgcataatcga ... tgttctgcagGCGATTGCTACCGAGGTGCAAAGTGAGTCCAAGTGGAAGATATTAGGGGAG
EST: gi|89106141|gb|DY576358.1|DY576358
EST:     ATTACAGATTTGACCTGGCTGTGCAACTTGGTCGACTTGAAATTGCGAAG                         GCGATTGCTACCGAGGTGCAAAGTGAGTCCAAGTGGAAGATATTAGGGGAG
genomic: ATTACAGATTTGACCTGGCTGTGCAACTTGGTCGACTTGAAATTGCGAAGgcataatcga ... tgttctgcagGCGATTGCTACCGAGGTGCAAAGTGAGTCCAAGTGGAAGATATTAGGGGAG
EST: gi|60337474|gb|DN204447.1|DN204447
EST:     ATTACAGATTTGACCTGGCTGTGCAACTTGGTCGACTTGAAATTGCGAAG                         GCGATTGCTACCGAGGTGCAAAGTGAGTCCAAGTGGAAGATATTAGGGGAG
genomic: ATTACAGATTTGACCTGGCTGTGCAACTTGGTCGACTTGAAATTGCGAAGgcataatcga ... tgttctgcagGCGATTGCTACCGAGGTGCAAAGTGAGTCCAAGTGGAAGATATTAGGGGAG
EST: gi|18649808|gb|BM498627.1|BM498627
EST:     ATTACAGATTTGACCTGGCTGTGCACCTTGGTCGACTTGAAATTGCGAAG                         GCGATTGCT-CCGAGGTGCAAAGTGAGTCCAAGTGGAAGATATTAGGGGAG
genomic: ATTACAGATTTGACCTGGCTGTGCAACTTGGTCGACTTGAAATTGCGAAGgcataatcga ... tgttctgcagGCGATTGCTACCGAGGTGCAAAGTGAGTCCAAGTGGAAGATATTAGGGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattttcgagaaagtatttcttttttgaatttttctaatagtagttgttctgcagGCGATTGCTACCGAGGTGCAAAGTGAGTCCAAGTGGAAGATATTAGGGGAGTTAGCTATGTCAAGTGGAAAG
                                ttctaat  putative branch site (score: 2)
                                            ttgttct  putative PPT
          aaagtatttctttttt  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcataatcgatttcttttcttctccacattttcgagaaagtatttcttttttgaatttttctaatagtagttgttctgcagGCGATTGCTACCGAGGTGCAAAGTGAGTCCAAGTGGAAGATATTAGGGGAGTTAGCTATGTCAAGTGGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA