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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgccagtgcactatttttcttgattcattcgcaatgaaattttattcagacgacgagggaaaattccgttgaccagacatcttgtttttcatgttctcagAGACAGCTACACCATTACCCTGGGGTACTAGGATGTCAATCGCACTGGGAGCTGCTAAAGGGCTTGCTTGCCTCCACAATGCTCAAAGGCCTGTCATCTA

Basic information

species Zea mays
transcript GRMZM2G007283_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G007283_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os12g02810.1 (Oryza sativa), 3'ss of exon 3
---tgccagtgcactatttttcttgattcattcgcaatgaaattttattcagacgacgagggaaaattccg---ttgaccagacatcttgtttttcatgttctcagAGACAGCTACACCATTACCCTGGGGTACTAGGATGTCAATCGCACTGGGAGCTGCTAAAGGGCTTGCTTGCCTCCACAATGCTCAAAGGCCTGTCATCTA
   |||      |   ||| |  |  | |||| |   |||| || ||||||   ||  ||| ||  ||| |   ||| |    | | |  ||||||   ||||||| ||||||||| ||| || |||||| |||||||||||| || ||| | || ||||| |||||| | |||||||||||||||||| |||||||  | |||||
ttgtgctcaactatattttgttcttgtacatt-gtggtgaacttgtattcaa--gattaggaaattttctgacattgtctgtgcttttcctttttc---ttctcagGGACAGCTACTCCACTATCCTGGGCTACTAGGATGTCGATTGCATTAGGGGCTGCCAAAGGGTTAGCTTGCCTCCACAATGCTGAAAGGCCAATTATCTA

upper sequence: GRMZM2G007283_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os11g02830.2 (Oryza sativa), 3'ss of exon 3
----tgccagtgcactatttttcttgattcattcgcaatgaaattttattcagacgacgagggaaaattccg---ttgaccagacatcttgtttttcatgttctcagAGACAGCTACACCATTACCCTGGGGTACTAGGATGTCAATCGCACTGGGAGCTGCTAAAGGGCTTGCTTGCCTCCACAATGCTCAAAGGCCTGTCATCTA
      | | |  | | ||||||||| | |||| |   ||||||| |||||    ||  ||| ||  | | |   ||| |    | | |  ||||||   ||||||| ||||||||| ||| || | |||| |||||||||||| || ||| | |||||||| |||||| | |||||||||||||||||| |||||||  | |||||
tatgctcaactatattttttttcttg-tacatt-gtggtgaaattgtattcga--gagtaggaaatttcctgacattgtctgtgcttttcatttttc---ttctcagGGACAGCTACTCCACTATCGTGGGCTACTAGGATGTCGATTGCATTAGGAGCTGCCAAAGGGTTAGCTTGCCTCCACAATGCTGAAAGGCCAATTATCTA

upper sequence: GRMZM2G007283_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT5G01020.1 (Arabidopsis thaliana), 3'ss of exon 2
------------tgccagtgcactatttt---tcttgattcattcgca---atgaaattttattcagacgacgagg---gaaaattccgttgaccagacatcttgtttttcatg-------ttctcagAGACAGCTACACCATTACCCTGGGGTACTAGGATGTCAATCGCACTGGGAGCTGCTAAAGGGCTTGCTTGCCTCCACAATGCTCAAAGGCCTGTCATCTA
              |   | || | |||    |||   |||||||  |   ||  ||  |||||| | |    ||    |  |    |||     |   | |    |   ||||       |  ||||| ||  |  | ||  || | |||  ||  ||||||   || || || |||||||| ||||| ||||||| ||||||||||||| |||| || || || ||
gtaatccccgcacccttctccattttttgaagtctctgttcattcctacatatacaagcttattctgccttttagtcttgtcatactcgtctcttatttaaccaagtcaccatgggctctctcttcagAAACCACAGCTCCGCTATCTTGGTCTAGAAGGATGATGATTGCTCTTGGAGCTGCGAAAGGCCTTGCTTTCCTCCACAATGCTGAAAGACCGGTTATTTA

upper sequence: GRMZM2G007283_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv08s0056g00150.t01 (Vitis vinifera), 3'ss of exon 3
----tgccagtg-cactatttttcttgat-tcattcgcaatgaaattttattcagacgacgagggaaaattccgttgaccagacatcttgtttttcatgttctcagAGACAGCTACACCATTACCCTGGGGTACTAGGATGTCAATCGCACTGGGAGCTGCTAAAGGGCTTGCTTGCCTCCACAATGCTCAAAGGCCTGTCATCTA
    | | |||| || ||  |    | || |  |||    | |    | ||      |     |  || |   |||||   | | |    |   | | |   |||||  |  ||   |||||| | ||||  |||||||||   || || ||||| ||||| ||||||||||||| |||||| |||||| |||||||||| |||||
tcaattctagtgacattacatgaagttatattgttcttcttaattcctcatat---tgtttctgttaactcaagttgatgtggcctt---tccctgaggcattcagAAGCGACTGTCCCATTATCTTGGGCAACTAGGATGATGATTGCTCTGGGTGCTGCGAAAGGGCTTGCTTTCCTCCATAATGCTGAAAGGCCTGTAATCTA

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|67022281|gb|CO451030.1|CO451030
EST:     TGTCTACGAGTTCATGTTTCGAGGAAGCCTAGAAAACCACCTATTCCGAA                         AGACAGCTACACCATTACCCTGNGGTACTAGGATGTCAATCGCACTGGGAG
genomic: TGTCTACGAGTTCATGTTTCGAGGAAGCCTAGAAAACCACCTATTCCGAAgtaatacttc ... atgttctcagAGACAGCTACACCATTACCCTGGGGTACTAGGATGTCAATCGCACTGGGAG
EST: gi|148957429|gb|EC903492.2|EC903492
EST:     TGTCTACGAGTTCATGTTTCGAGGAAGCCTAGAAAACCACCTATTCCGAA                         AGACAGCTACACCATTACCCTGGGGTACTAGGATGTCAATCGCACTGGGAG
genomic: TGTCTACGAGTTCATGTTTCGAGGAAGCCTAGAAAACCACCTATTCCGAAgtaatacttc ... atgttctcagAGACAGCTACACCATTACCCTGGGGTACTAGGATGTCAATCGCACTGGGAG
EST: gi|74234771|gb|DT642685.1|DT642685
EST:     TGTCTACGAGTTCATGTTTCGAGGAAGCCTAGAAAACCACCTATTCCGAA                         AGACAGCTACACCATTACCCTGGGGTACTAGGATGTCAATCGGACTGGCAG
genomic: TGTCTACGAGTTCATGTTTCGAGGAAGCCTAGAAAACCACCTATTCCGAAgtaatacttc ... atgttctcagAGACAGCTACACCATTACCCTGGGGTACTAGGATGTCAATCGCACTGGGAG
EST: gi|78081509|gb|DV509921.1|DV509921
EST:     TGTCTACGAGTTCATGTTTCGAGGAAGCCTAGAAAACCACCTATTCCGAA                         AGACAGCTACACCATTACCCTGGGGTACTAGGATGTCAATCGCACTGGGAG
genomic: TGTCTACGAGTTCATGTTTCGAGGAAGCCTAGAAAACCACCTATTCCGAAgtaatacttc ... atgttctcagAGACAGCTACACCATTACCCTGGGGTACTAGGATGTCAATCGCACTGGGAG
EST: gi|74234770|gb|DT642684.1|DT642684
EST:     TGTCTACGAGTTCATGTTTCGAGGAAGCCTAGAAAACCACCTATTCCGAA                         AGACAGCTACACCATTACCCTGGGGTACTAGGATGTCAATCGCACTGGGAG
genomic: TGTCTACGAGTTCATGTTTCGAGGAAGCCTAGAAAACCACCTATTCCGAAgtaatacttc ... atgttctcagAGACAGCTACACCATTACCCTGGGGTACTAGGATGTCAATCGCACTGGGAG
EST: gi|149102573|gb|EE188233.2|EE188233
EST:     TGTCTACGAGTTCATGTTTCGAGGAAGCCTAGAAAACCACCTATTCCGAA                         AGACAGCTACACCATTACCCTGGGGTACTAGGATGTCAATCGCACTGGGAG
genomic: TGTCTACGAGTTCATGTTTCGAGGAAGCCTAGAAAACCACCTATTCCGAAgtaatacttc ... atgttctcagAGACAGCTACACCATTACCCTGGGGTACTAGGATGTCAATCGCACTGGGAG
EST: gi|71437207|gb|DR818257.1|DR818257
EST:     TGTCTACGAGTTCATGTTTCGAGGAAGCCTAGAAAACCACCTATTCCGAA                         AGACAGCTACACCATTACCCTGGGGTACTAGGATGTCAATCGCACTGGGAG
genomic: TGTCTACGAGTTCATGTTTCGAGGAAGCCTAGAAAACCACCTATTCCGAAgtaatacttc ... atgttctcagAGACAGCTACACCATTACCCTGGGGTACTAGGATGTCAATCGCACTGGGAG
EST: gi|71315550|gb|DR794379.1|DR794379
EST:     TGTCTACGAGTTCATGTTTCGAGGAAGCCTAGAAAACCACCTATTCCGAA                         AGACAGCTACACCATTACTCTGGGGTACTAGGATGTCAATCGCACTGGGAG
genomic: TGTCTACGAGTTCATGTTTCGAGGAAGCCTAGAAAACCACCTATTCCGAAgtaatacttc ... atgttctcagAGACAGCTACACCATTACCCTGGGGTACTAGGATGTCAATCGCACTGGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagacgacgagggaaaattccgttgaccagacatcttgtttttcatgttctcagAGACAGCTACACCATTACCCTGGGGTACTAGGATGTCAATCGCACTGGGAGCTGCTAAAGGGCTTGCTTGCCTCCACAATGCTCAAAGGCCTGTCATCTA
                     cgttgac  putative branch site (score: 4)
                                       tttttcatgttctc  putative PPT
                                    ttgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgccagtgcactatttttcttgattcattcgcaatgaaattttattcagacgacgagggaaaattccgttgaccagacatcttgtttttcatgttctcagAGACAGCTACACCATTACCCTGGGGTACTAGGATGTCAATCGCACTGGGAGCTGCTAAAGGGCTTGCTTGCCTCCACAATGCTCAAAGGCCTGTCATCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT