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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gactcgagtactgcatgtacataacttctgtctcatttctaaggtagtaaagcaaatatgccgtgtttaaaaatgtaaattcttacacttgctttcacagGTGGTGCCATCAGTAGCCATAGGATTTACTGTTTACGACTCGATGAAGGTCTGTCTAAAAGTTCCGTCGAGGGAGGAAACTGCTGTTGCTGTCTTGGCAG

Basic information

species Zea mays
transcript GRMZM2G161299_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G161299_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g13300.2 (Oryza sativa), 3'ss of exon 6
-gactcgagtactgcatgtacataacttctgtctcatttctaaggtagtaaagcaaatatgccgtgtttaaaaatgtaaattcttaca-cttgctttcacagGTGGTGCCATCAGTAGCCATAGGATTTACTGTTTACGACTCGATGAAGGTCTGTCTAAAAGTTCCGTCGAGGGAGGAAACTGCTGTTGCTGTCTTGGCAG
  | |    ||    |||| |||  || || |    ||   ||||||       |  || | |  |    ||| | ||  |||  |   ||   ||| ||||||||| ||||||||||||||||| ||||| ||||| ||||| |||||||| || || |||||||| ||||| ||||| || ||| ||||||   || |||
aaaattacataagtaatgttcat--ctccttttgtgttaagaaggtacctctctagttaaggctagaggcaaagtatatcttcacaagtctctttttgacagGTGGTCCCATCAGTAGCCATAGGGTTTACAGTTTATGACTCAATGAAGGTTTGGCTTAAAGTTCCATCGAGAGAGGACACGGCTATTGCTGCGCTGACAG
















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|67010867|gb|CO439616.1|CO439616
EST:     AGCAAGGCTGGCGACAACTTTTCTCAGGATTATCTATCAACTATTTAAAG                         GTGGTGCCATCAGTAGCCATAGGATTTACTGTTTACGACTCGATGAAGGTC
genomic: AGCAAGGCTGGCGACAACTTTTCTCAGGATTATCTATCAACTATTTAAAGgtgagatatt ... gctttcacagGTGGTGCCATCAGTAGCCATAGGATTTACTGTTTACGACTCGATGAAGGTC
EST: gi|16926745|gb|BM079813.1|BM079813
EST:     AGCAAGGCTGGCGACAACTTTTCTCAGGATTATCTATCAACTATTTAAAG                         GTGGTGCCATCAGTAGCCATAGGATTTACTGTTTACGACTCGATGAAGGTC
genomic: AGCAAGGCTGGCGACAACTTTTCTCAGGATTATCTATCAACTATTTAAAGgtgagatatt ... gctttcacagGTGGTGCCATCAGTAGCCATAGGATTTACTGTTTACGACTCGATGAAGGTC
EST: gi|71761231|gb|DR959168.1|DR959168
EST:     AGCAAGGCTGGCGACAACTTTTCTCAGGATTATCTATCAACTATTTAAAG                         GTGGTGCCATCAGTAGCCATAGGATTTACTGTTTACGACTCGATGAAGGTC
genomic: AGCAAGGCTGGCGACAACTTTTCTCAGGATTATCTATCAACTATTTAAAGgtgagatatt ... gctttcacagGTGGTGCCATCAGTAGCCATAGGATTTACTGTTTACGACTCGATGAAGGTC
EST: gi|76294059|gb|DV033627.1|DV033627
EST:     AGCAAGGCTGGCGACAACTTTTCTCAGGATTATCTATCAACTATTTAAAG                         GTGGTGCCATCAGTAGCCATAGGATTTACTGTTTACGACTCGATGAAGGTC
genomic: AGCAAGGCTGGCGACAACTTTTCTCAGGATTATCTATCAACTATTTAAAGgtgagatatt ... gctttcacagGTGGTGCCATCAGTAGCCATAGGATTTACTGTTTACGACTCGATGAAGGTC
EST: gi|71435374|gb|DR816424.1|DR816424
EST:     AGCAAGGCTGGCGACAACTTTTCTCAGGATTATCTATCAACTATTTAAAG                         GTGGTGCCATCAGTAGCCATAGGATTTACTGTTTACGACTCGATGAAGGTC
genomic: AGCAAGGCTGGCGACAACTTTTCTCAGGATTATCTATCAACTATTTAAAGgtgagatatt ... gctttcacagGTGGTGCCATCAGTAGCCATAGGATTTACTGTTTACGACTCGATGAAGGTC
EST: gi|94477872|gb|EB706830.1|EB706830
EST:     AGCAAGGCTGGCGACAACTTTTCTCAGGATTATCTATCAACTATTTAAAG                         GTGGTGCCATCAGTAGCCATAGGATTTACTGTTTACGACTCGATGAAGGTC
genomic: AGCAAGGCTGGCGACAACTTTTCTCAGGATTATCTATCAACTATTTAAAGgtgagatatt ... gctttcacagGTGGTGCCATCAGTAGCCATAGGATTTACTGTTTACGACTCGATGAAGGTC
EST: gi|71757614|gb|DR955551.1|DR955551
EST:     AGCAAGGCTGGCGACAACTTTTCTCAGGATTATCTATCAACTATTTAAAG                         GTGGTGCCATCAGTAGCCATAGGATTTACTGTTTACGACTCGATGAAGGTC
genomic: AGCAAGGCTGGCGACAACTTTTCTCAGGATTATCTATCAACTATTTAAAGgtgagatatt ... gctttcacagGTGGTGCCATCAGTAGCCATAGGATTTACTGTTTACGACTCGATGAAGGTC
EST: gi|71442969|gb|DR824019.1|DR824019
EST:     AGCAAGGCTGGCGACAACTTTTCTCAGGATTATCTATCAACTATTTAAAG                         GTGGTGCCATCAGTAGCCATAGGATTTACTGTTTACGACTCGATGAAGGTC
genomic: AGCAAGGCTGGCGACAACTTTTCTCAGGATTATCTATCAACTATTTAAAGgtgagatatt ... gctttcacagGTGGTGCCATCAGTAGCCATAGGATTTACTGTTTACGACTCGATGAAGGTC
EST: gi|38687748|gb|CK144779.1|CK144779
EST:     CAACTTTTCTCAGGATTATCTATCAACTATTTAAAG                         GTGGTGCCATCAGTAGCCATAGGATTTACTGTTTACGACTCGATGAAGGTC
genomic: CAACTTTTCTCAGGATTATCTATCAACTATTTAAAGgtgagatatt ... gctttcacagGTGGTGCCATCAGTAGCCATAGGATTTACTGTTTACGACTCGATGAAGGTC
EST: gi|71760931|gb|DR958868.1|DR958868
EST:     AGCAAGGCTGGCGACAACTTTTCTCAGGATTATCTATCAACTATTTAAAG                         GTGGTGCCATCAGTAGCCATAGGATTTACTGTTTACGACTCGATGAAGGTC
genomic: AGCAAGGCTGGCGACAACTTTTCTCAGGATTATCTATCAACTATTTAAAGgtgagatatt ... gctttcacagGTGGTGCCATCAGTAGCCATAGGATTTACTGTTTACGACTCGATGAAGGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtaaagcaaatatgccgtgtttaaaaatgtaaattcttacacttgctttcacagGTGGTGCCATCAGTAGCCATAGGATTTACTGTTTACGACTCGATGAAGGTCTGTCTAAAAGTTCCGTCGAGGGAGGAAACTGCTGTTGCTGTCTTGGCAG
                                  ttcttac  putative branch site (score: 2)
                                          cttgctttc  CT-rich tract
                  tgtttaaaaatgtaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gactcgagtactgcatgtacataacttctgtctcatttctaaggtagtaaagcaaatatgccgtgtttaaaaatgtaaattcttacacttgctttcacagGTGGTGCCATCAGTAGCCATAGGATTTACTGTTTACGACTCGATGAAGGTCTGTCTAAAAGTTCCGTCGAGGGAGGAAACTGCTGTTGCTGTCTTGGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT