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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggtttccttggacacattatgcttttttttttacattgatctggcaacccatctttagtcttttgccattcactaagtttcattcgctttgttccagGTTCGTGATTTTGAGTATAGTCCTGAAGCACAAGAAAGTAGAAAGCAGGAGATGGAGAAGTTACTGCTAGAGCAGGAAGTTATGAGGACCTCGCTTCTGC

Basic information

species Zea mays
transcript GRMZM2G177912_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G177912_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os05g51530.1 (Oryza sativa), 3'ss of exon 7
----------------------------------------------------------------------------------gtaaggtttccttggacacattatgcttttttttttacattgatctggcaacccatctttagtcttttgccattcactaagtttcatt-cgctttgttccagGTTCGTGATTTTGAGTATAGTCCTGAAGCACAAGAAAGTAGAAAGCAGGAGATGGAGAAGTTACTGCTAGAGCAGGAAGTTATGAGGACCTCGCTTCTGC
                                                                                     |  |  | | ||||| |  || |  | || |||   |    |   ||| |   |   | |  | || ||  || ||| ||  ||| || |    | |||||||| ||||||||||||||| |||||||||| |||||||| ||| | ||| |||| ||| || ||| ||| |||||||  |||||| | || |||||||
gtaaatttgccgtcctaactttttcatcaaaaacctttgtttacacttcacatttagcttttatccctagagccttaggagttccaaataacttgggacagaa-attcagtcttgtttttctgtccccatcaatctggc---aattctctgtcacccattaacttgtattacgttgaaatacagGTTCGCGATTTTGAGTATAGTTCTGAAGCACAGGAAAGTAGGAAGGAAGAGCTGGAAAAGCTAATGCAAGACCAGGAAGCAATGAGGGCATCACTTCTGC

upper sequence: GRMZM2G177912_T02 (Zea mays), 3'ss of exon 7
lower sequence: Vv17s0000g00460.t01 (Vitis vinifera), 3'ss of exon 7
------gtaaggtt-tccttggacacattatgcttttttttttacattgatctggcaacccatctttagtcttttgccattcactaagtttcattcgctttgttccagGTTCGTGATTTTGAGTATAGTCCTGAAGCACAAGAAAGTAGAAAGCAGGAGATGGAGAAGTTACTGCTAGAGCAGGAAGTTATGAGGACCTCGCTTCTGC
      | | |  | |    ||| | ||||     ||   | ||  |||   |||    |  |   || |  | ||  ||   | |  ||||||  | ||     ||| ||||||||||||| |||||||| ||| ||||||| ||||| ||||||||| |||| ||  |  ||||||| |||||    || || ||||| ||| |||
aaaaaggcaggaatataacaggataaattaacacattcaatataatttg--ttggagttctcttcctaatgatctgt-atgttcaatttttcatgtgatt-----cagATTCGTGATTTTGAATATAGTCCAGAAACACAAGAGAGTAGGAAGCAGGAGTTGGAAAAACTGATGCTAGATCAGGACACGATTAGAACCTCTCTTTTGC
















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|148969237|gb|EE019991.2|EE019991
EST:     CTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTCCAG                         GTTCGTGATTTTGAGTATAGTCCTGAAGCACAAGAAAGTAGAAAGCAGGAG
genomic: CTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTCCAGgtaaggtttc ... tttgttccagGTTCGTGATTTTGAGTATAGTCCTGAAGCACAAGAAAGTAGAAAGCAGGAG
EST: gi|76288289|gb|DV027857.1|DV027857
EST:     ACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTCCAG                         GTTCGTGATTTTGAGTATAGTCCTGAAGCACAAGAAAGTAGAAAGCAGGAG
genomic: ACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTCCAGgtaaggtttc ... tttgttccagGTTCGTGATTTTGAGTATAGTCCTGAAGCACAAGAAAGTAGAAAGCAGGAG
EST: gi|60340364|gb|DN207337.1|DN207337
EST:     CTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTCCAG                         GTTCGTGATTTTGAGTATAGTCCTGAAGCACAAGAAAGTAGAAAGCAGGAG
genomic: CTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTCCAGgtaaggtttc ... tttgttccagGTTCGTGATTTTGAGTATAGTCCTGAAGCACAAGAAAGTAGAAAGCAGGAG
EST: gi|67016433|gb|CO445182.1|CO445182
EST:     CTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTNCAG                         ATTCGTGATTTTGAGTATAGTCCTGAAGCACAAGAAAGT
genomic: CTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTCCAGgtaaggtttc ... tttgttccagGTTCGTGATTTTGAGTATAGTCCTGAAGCACAAGAAAGT
EST: gi|40337132|gb|CK371202.1|CK371202
EST:     CTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTCCAG                         GTTCGTGATTTTGAGTATAGTCCTGAAGCACAAGAAAGTAGAAAGCAGGAG
genomic: CTAAGGTTGTTGACAACTTTAAGGTCCGTGCTCGCGAGAAGGGTTTCCAGgtaaggtttc ... tttgttccagGTTCGTGATTTTGAGTATAGTCCTGAAGCACAAGAAAGTAGAAAGCAGGAG
EST: gi|71327561|gb|DR800389.1|DR800389
EST:     TAAGGTTGTTGACAACTTTAAAGGTCCGTGCTCGCGAGAAGGGTTTCCAG                         GTTCGTGATTTTGAGTATAGTCCTGAAGCACAAGAAAGTAGAAAGCAGGAG
genomic: TAAGGTTGTTGACAACTTT-AAGGTCCGTGCTCGCGAGAAGGGTTTCCAGgtaaggtttc ... tttgttccagGTTCGTGATTTTGAGTATAGTCCTGAAGCACAAGAAAGTAGAAAGCAGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcaacccatctttagtcttttgccattcactaagtttcattcgctttgttccagGTTCGTGATTTTGAGTATAGTCCTGAAGCACAAGAAAGTAGAAAGCAGGAGATGGAGAAGTTACTGCTAGAGCAGGAAGTTATGAGGACCTCGCTTCTGC
                                            ctttgttcc  CT-rich tract
        atcttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggtttccttggacacattatgcttttttttttacattgatctggcaacccatctttagtcttttgccattcactaagtttcattcgctttgttccagGTTCGTGATTTTGAGTATAGTCCTGAAGCACAAGAAAGTAGAAAGCAGGAGATGGAGAAGTTACTGCTAGAGCAGGAAGTTATGAGGACCTCGCTTCTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG