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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacaaaatctacagagcttttccttattggggttcttgctaatggtgcactcaatcctttggtatgatggttgaccgactgtctcaacttgttcccacagGACGCTGTTTCACTTGTGAAGATGGAGGAGGATCCTGAGGCAGCAGCCCGGAAGCTGACAGAGACTGCGTTCTCCCGTGGGAGCGGCGATAACATCACCT

Basic information

species Zea mays
transcript GRMZM2G158818_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G158818_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os05g50970.1 (Oryza sativa), 3'ss of exon 8
aacaaaatctacagagcttttccttattggggt----tcttgctaatggtgcactc-aatcctttggtatgatggttgaccgactgtctcaacttgttcccacagGACGCTGTTTCACTTGTGAAGATGGAGGAGGATCCTGAGGCAGCAGCCCGGAAGCTGACAGAGACTGCGTTCTCCCGTGGGAGCGGCGATAACATCACCT
     |    | |  |  |   || |||  | |    ||||| | || ||||| |  ||  | | | ||    |  | | ||  | ||||    ||||    ||||| ||||||||||| |||||||| |||||||| |||||||||||||| |||||||||||||||||||| || ||||| ||||| || || || ||||| |
----catgtcataatggataatctaattatgctcccctcttgttcatagtgcattttaaaacatagttaattcgcctcatcgtgtttctcc-tatgttgatgcagGATGCTGTTTCACTCGTGAAGATTGAGGAGGAACCTGAGGCAGCAGCTCGGAAGCTGACAGAGACTGCATTTTCCCGAGGGAGTGGTGACAATATCACAT
















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|71770125|gb|DR968062.1|DR968062
EST:     AGTTTCTAATTATAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAG                         GACGCTGTTTCACTTGTGAAGATGGAGGAGGATCCTGAGGCAGCAGCCCGG
genomic: AGTTTCTAATTATAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAGgttagtttgt ... gttcccacagGACGCTGTTTCACTTGTGAAGATGGAGGAGGATCCTGAGGCAGCAGCCCGG
EST: gi|20301082|gb|BQ164025.1|BQ164025
EST:     AGTTTCTAATTATAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAG                         GACGCTGTTTCACTTGTGAAGATGGAGG
genomic: AGTTTCTAATTATAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAGgttagtttgt ... gttcccacagGACGCTGTTTCACTTGTGAAGATGGAGG
EST: gi|211312460|gb|FL459524.1|FL459524
EST:     AGTTTCTAATTATAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAG                         GACGCTGTTTCACTTGTGAAGATGGAGGAGGATCCTGAGGCAGCAGCCCGG
genomic: AGTTTCTAATTATAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAGgttagtttgt ... gttcccacagGACGCTGTTTCACTTGTGAAGATGGAGGAGGATCCTGAGGCAGCAGCCCGG
EST: gi|78024801|gb|DV493188.1|DV493188
EST:     TTATAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAG                         GACGCTGTTTCACTTGTGAAGATGGAGGAGGATCCTGAGGCAGCAGCCCGG
genomic: TTATAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAGgttagtttgt ... gttcccacagGACGCTGTTTCACTTGTGAAGATGGAGGAGGATCCTGAGGCAGCAGCCCGG
EST: gi|149098862|gb|EE184875.2|EE184875
EST:     AGTTTCTAATTATAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAG                         GACGCTGTTTCACTTGTGAAGATGGAGGAGGATCCTGAGGCAGCAGCCCGG
genomic: AGTTTCTAATTATAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAGgttagtttgt ... gttcccacagGACGCTGTTTCACTTGTGAAGATGGAGGAGGATCCTGAGGCAGCAGCCCGG
EST: gi|211050684|gb|FL481891.1|FL481891
EST:     AGTTTCTAATTATAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAG                         GACGCTGTTTCACTTGTGAAGATGGAGGAGGATCCTGAGGCAGCAGCCCGG
genomic: AGTTTCTAATTATAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAGgttagtttgt ... gttcccacagGACGCTGTTTCACTTGTGAAGATGGAGGAGGATCCTGAGGCAGCAGCCCGG
EST: gi|67022511|gb|CO451260.1|CO451260
EST:     AGTTTCTAATTATAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAG                         GACGCTGTTTCACTTGTGAAGATGGAGGAGGATCCTGAGGCAGCAGCCCGG
genomic: AGTTTCTAATTATAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAGgttagtttgt ... gttcccacagGACGCTGTTTCACTTGTGAAGATGGAGGAGGATCCTGAGGCAGCAGCCCGG
EST: gi|211331038|gb|FL445937.1|FL445937
EST:     AGTTTCTAATTATAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAG                         GACGCTGTTTCACTTGTGAAGATGGAGGAGGATCCTGAGGCAGCAGCCCGG
genomic: AGTTTCTAATTATAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAGgttagtttgt ... gttcccacagGACGCTGTTTCACTTGTGAAGATGGAGGAGGATCCTGAGGCAGCAGCCCGG
EST: gi|4804314|gb|AI666180.1|AI666180
EST:     ATGGGCTGTGGGATGTGGTTCCGAATGAG                         GACGCTGTTTCACTTGTGAAGATGGAGGAGGATCCTGAGGCAGCAGCCCGG
genomic: ATGGGCTGTGGGATGTGGTTCCGAATGAGgttagtttgt ... gttcccacagGACGCTGTTTCACTTGTGAAGATGGAGGAGGATCCTGAGGCAGCAGCCCGG
EST: gi|32795938|gb|CD948174.1|CD948174
EST:     AGTTTCTAATTATAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAG                         GACGCTGTTTCACTTGTGAAGATGGAGGAGGATC
genomic: AGTTTCTAATTATAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAGgttagtttgt ... gttcccacagGACGCTGTTTCACTTGTGAAGATGGAGGAGGATC
EST: gi|9733204|gb|BE511956.1|BE511956
EST:     AGTTTCTAATTATAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAG                         GACGCTGTTTCACTTGTGAAGATGGAGGAGGATCCTGAGGCAGCAGCCCGG
genomic: AGTTTCTAATTATAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAGgttagtttgt ... gttcccacagGACGCTGTTTCACTTGTGAAGATGGAGGAGGATCCTGAGGCAGCAGCCCGG
EST: gi|101388859|gb|EB816411.1|EB816411
EST:     AGTTTCTAATTATAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAG                         GACGCTGTTTCACTTGTGAAGATGGAGGAGGATCCTGAGGCAGCAGCCCGG
genomic: AGTTTCTAATTATAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAGgttagtttgt ... gttcccacagGACGCTGTTTCACTTGTGAAGATGGAGGAGGATCCTGAGGCAGCAGCCCGG
EST: gi|19058198|gb|BM736865.1|BM736865
EST:     AGTTTCTAATTATAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAG                         GACGCTGTTTCACTTGTGAAGATGGAGG
genomic: AGTTTCTAATTATAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAGgttagtttgt ... gttcccacagGACGCTGTTTCACTTGTGAAGATGGAGG
EST: gi|211345077|gb|FL234318.1|FL234318
EST:     AGTTTCTAATTATAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAG                         GACGCTGTTTCACTTGTGAAGATGGAGGAGGATCCTGAGGCAGCAGCCCGG
genomic: AGTTTCTAATTATAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAGgttagtttgt ... gttcccacagGACGCTGTTTCACTTGTGAAGATGGAGGAGGATCCTGAGGCAGCAGCCCGG
EST: gi|20300882|gb|BQ163825.1|BQ163825
EST:     AGTTTCTAATTATAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAG                         GACGCTGTTTCACTTGTGAAGATGGAGG
genomic: AGTTTCTAATTATAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAGgttagtttgt ... gttcccacagGACGCTGTTTCACTTGTGAAGATGGAGG
EST: gi|211018239|gb|FL446511.1|FL446511
EST:     AGTTTCTAATTATAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAG                         GACGCTGTTTCACTTGTGAAGATGGAGGAGGATCCTGAGGCAGCAGCCCGG
genomic: AGTTTCTAATTATAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAGgttagtttgt ... gttcccacagGACGCTGTTTCACTTGTGAAGATGGAGGAGGATCCTGAGGCAGCAGCCCGG
EST: gi|9961513|gb|BE644301.1|BE644301
EST:     AGTTTCTAATTATAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAG                         GACGCTGTTTCACTTGTGAAGATGGAGGAGGATCCTGAGGCAGCAGCCCGG
genomic: AGTTTCTAATTATAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAGgttagtttgt ... gttcccacagGACGCTGTTTCACTTGTGAAGATGGAGGAGGATCCTGAGGCAGCAGCCCGG
EST: gi|211342699|gb|FL234316.1|FL234316
EST:     AGTTTCTAATTATAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAG                         GACGCTGTTTCACTTGTGAAGATGGAGGAGGATCCTGAGGCAGCAGCCCGG
genomic: AGTTTCTAATTATAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAGgttagtttgt ... gttcccacagGACGCTGTTTCACTTGTGAAGATGGAGGAGGATCCTGAGGCAGCAGCCCGG
EST: gi|40336649|gb|CK370719.1|CK370719
EST:     GGGCTGTGGGATGTGGTTCCGAATGAG                         GACGCTGTTTCACTTGTGAAGATGGAGGAGGATCCTGAGGCAGCAGCCCGG
genomic: GGGCTGTGGGATGTGGTTCCGAATGAGgttagtttgt ... gttcccacagGACGCTGTTTCACTTGTGAAGATGGAGGAGGATCCTGAGGCAGCAGCCCGG
EST: gi|61119350|gb|DN560311.1|DN560311
EST:     AGTTTCTAATTATAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAG                         GACGCTGTTTCACTTGTGAAGATGGAGGAGGATCCTGAGGCAGCAGCCCGG
genomic: AGTTTCTAATTATAGCTAGTGATGGGCTGTGGGATGTGGTTCCGAATGAGgttagtttgt ... gttcccacagGACGCTGTTTCACTTGTGAAGATGGAGGAGGATCCTGAGGCAGCAGCCCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcactcaatcctttggtatgatggttgaccgactgtctcaacttgttcccacagGACGCTGTTTCACTTGTGAAGATGGAGGAGGATCCTGAGGCAGCAGCCCGGAAGCTGACAGAGACTGCGTTCTCCCGTGGGAGCGGCGATAACATCACCT
                       ggttgac  putative branch site (score: 4)
                                          cttgttccc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacaaaatctacagagcttttccttattggggttcttgctaatggtgcactcaatcctttggtatgatggttgaccgactgtctcaacttgttcccacagGACGCTGTTTCACTTGTGAAGATGGAGGAGGATCCTGAGGCAGCAGCCCGGAAGCTGACAGAGACTGCGTTCTCCCGTGGGAGCGGCGATAACATCACCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
aacaaaa
- - - - - - - - - - - - - - - - ttcttgc
- - - - - - - - - - - - - - - - - - - - - -ggtgcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatgatg