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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttaccgctgctgctttttttgttcatttctcgttttacttatgtgcttgcctcacggtattttggtgctgtactcttttagATATGTTTGGGAATCAAAAGCTGATGGATCGTTTGCTATCTCCGAGGATACATGGAATGAACCCCTTGGCCGTGGAACCGAGATAAGATTACATCTGCGA

Basic information

species Zea mays
transcript GRMZM2G399073_T03
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G399073_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os06g50300.1 (Oryza sativa), 3'ss of exon 6
----------------gta-agttaccgc-tgctgctttttttgttcatt---tctcgttttacttatgtgcttgcct-cacggtattttggtgctgtactcttt------tagATATGTTTGGGAATCAAAAGCTGATGGATCGTTTGCTATCTCCGAGGATACATGGAATGAACCCCTTGGCCGTGGAACCGAGATAAGATTACATCTGCGA
                 || ||   |  | |  ||  ||||| ||||||    | |   || |||    ||    ||| |    | || || || || ||| |||      |||  |||| ||||| || |||||||||||||| || |||||||| ||||||||||||||||||||||| ||||||||||| || |||||| | || || |||
gtaagacaccactgaaatacagcggctacatattgtgtttttggttcatcttcttttccttcactggcatgacaacctacttcatgttctgctgttgcactttttctctgatagGCATGTCTGGGAGTCCAAAGCTGATGGATCATTCGCTATCTCTGAGGATACATGGAATGAACCCCTGGGCCGTGGAACTGAAATAAGACTGCACCTCCGA

upper sequence: GRMZM2G399073_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 6
-gtaagttaccgctgctgctttttttgttcatttctcgttttacttatgtgcttgcctcacggtattttggtgctgtactctttt-agATATGTTTGGGAATCAAAAGCTGATGGATCGTTTGCTATCTCCGAGGATACATGGAATGAACCCCTTGGCCGTGGAACCGAGATAAGATTACATCTGCGA
 ||||||      ||   ||  | | |||  ||| |   || |||| |   |  ||     |  | ||      | | |  |||| || ||||| ||||||||||||||||||||| | ||||| || || || ||||||||||||||||| || || |||||||| ||||| |||||||| || | |
agtaagtc-tttttggacctgatatcgtt--tttgtttgttgacttgtaacccagctatctg--acttgaaaattattcggttttcaGGTATGTATGGGAATCAAAAGCTGATGGAGCATTTGCAATTTCAGAAGATACATGGAATGAACCTCTAGGGCGTGGAACTGAGATTAGATTACACCT-CAA

upper sequence: GRMZM2G399073_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA14G40320.1 (Glycine max), 3'ss of exon 6
gtaagttaccg-----ctgctgctttttttgt--tcatttctcgtt------------ttacttatgtgcttgcctcacgg-----tattttggtgctgtact--cttttagATATGTTTGGGAATCAAAAGCTGATGGATCGTTTGCTATCTCCGAGGATACATGGAATGAACCCCTTGGCCGTGGAACCGAGATAAGATTACATCTGCGA
||||||          ||| || | |||||||  ||| ||    ||            ||  || |   ||||   | | |     ||  |||   ||    |   ||| || ||||| ||||||||||||||||||||| | || ||||| || || ||||||||||||||||| ||||| || ||||| ||||| |||||||| ||    
gtaagtccttttggacctgatgttgtttttgtaatcagttagtattgaaggaaaatttttgtttgttgacttgtaacccagctgcctaacttgaaacttatttggttttcagGTATGTATGGGAATCAAAAGCTGATGGAGCATTCGCTATTTCAGAAGATACATGGAATGAACCACTTGGACGAGGAACTGAGATTAGATTACACCTCAAG

upper sequence: GRMZM2G399073_T03 (Zea mays), 3'ss of exon 6
lower sequence: AT4G24190.2 (Arabidopsis thaliana), 3'ss of exon 6
gtaagttaccgctgctg-ctttttttgttcatttctcgttttacttatgtgcttgcctcacggtattttgg------tgctgtactcttttagATATGTTTGGGAATCAAAAGCTGATGGATCGTTTGCTATCTCCGAGGATACATGGAATGAACCCCTTGGCCGTGGAACCGAGATAAGATTACATCTGCGA
|||||||      |  | |||| ||||   || |     |   | | |    |      |  |  |||  |      |  | | |  ||| || ||||| ||||||||||| ||| | ||    |||||| | |||||||||||||||||||| || ||||| |||||||||||||| |||||||||||  | 
gtaagttgatttagagggctttgtttggcaatatacttgtgggcatgtaaaatcattgaaaagcttttctgataacttcttttccgttttcagGTATGTATGGGAATCAAAGGCTAACGGTAAATTTGCTGTTTCCGAGGATACATGGAATGAGCCTCTTGGACGTGGAACCGAGATTAGATTACATCTTAGG

upper sequence: GRMZM2G399073_T03 (Zea mays), 3'ss of exon 6
lower sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 6
-----------------gtaagttaccgctgctgctttttttgttcatttctcgttttacttatgtgcttgcctcacggtattttggtgctgta----ctcttttagATATGTTTGGGAATCAAAAGCTGATGGATCGTTTGCTATCTCCGAGGATACATGGAATGAACCCCTTGGCCGTGGAACCGAGATAAGATTACATCTGCGA
                  | | ||     |  |  | || || ||  ||| |  | | |   |   | ||     | ||  |  || |  |  |      | || || ||||| ||||| || |||||||||||| | ||||| || || ||||||  |||||||||||| || || |||||||| ||||| ||||| |||||  ||
gtgagcctcttgaagattttattttattttatttttattattattttttttttttgtgaaccagaggtttatgaaatggattgatgatcattcaaatttccattcagGTATGTATGGGAGTCTAAAGCTGATGGAGCTTTTGCAATTTCTGAGGATGTATGGAATGAACCACTCGGACGTGGAACTGAGATCAGATTGCATCTCAGA

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|148965480|gb|EE016290.2|EE016290
EST:     TTGGTTGCTGACTATGTCGAAGTGGTCAGCAAGCACAATGATGATAAACA                         ATATGTTTGGGAATCAAAAGCTGATGGATCGTTTGCTATCTCCGAGGATAC
genomic: TTGGTTGCTGACTATGTCGAAGTGGTCAGCAAGCACAATGATGATAAACAgtaagttacc ... actcttttagATATGTTTGGGAATCAAAAGCTGATGGATCGTTTGCTATCTCCGAGGATAC
EST: gi|56538364|gb|CX054073.1|CX054073
EST:     TTAGTTGCTGACTATGTCGAAGTGGTCAGCAAGCACAATGATGATAAACA                         ATATGTTTGGGAATCAAAAGCTGATGGATCATTTGCTATCTCCGAGGATAC
genomic: TTGGTTGCTGACTATGTCGAAGTGGTCAGCAAGCACAATGATGATAAACAgtaagttacc ... actcttttagATATGTTTGGGAATCAAAAGCTGATGGATCGTTTGCTATCTCCGAGGATAC
EST: gi|149004856|gb|EE039364.2|EE039364
EST:     TTGGTTGCTGACTATGTCGAAGTGGTCAGCAAGCACAATGATGATAAACA                         ATATGTTTGGGAATCAAAAGCTGATGGATCGTTTGCTATCTCCGAGGATAC
genomic: TTGGTTGCTGACTATGTCGAAGTGGTCAGCAAGCACAATGATGATAAACAgtaagttacc ... actcttttagATATGTTTGGGAATCAAAAGCTGATGGATCGTTTGCTATCTCCGAGGATAC
EST: gi|24767582|gb|CA402726.1|CA402726
EST:     TTGGTTGCTGACTATGTCGAAGTGGTCAGCAAGCACAATGATGATAAACA                         ATATGTGTGGGAATCAAAAGCTGATGGATCATTTGCTATCTCTGAGGATAC
genomic: TTGGTTGCTGACTATGTCGAAGTGGTCAGCAAGCACAATGATGATAAACAgtaagttacc ... actcttttagATATGTTTGGGAATCAAAAGCTGATGGATCGTTTGCTATCTCCGAGGATAC
EST: gi|31360086|gb|CD444443.1|CD444443
EST:     TTGGTTGCTGACTATGTCGAAGTGGTCAGCAAGCACAATGATGATAAACA                         ATATGTGTGGGAATCAAAAGCTGATGGATCATTTGCTATCTCTGAGGATAC
genomic: TTGGTTGCTGACTATGTCGAAGTGGTCAGCAAGCACAATGATGATAAACAgtaagttacc ... actcttttagATATGTTTGGGAATCAAAAGCTGATGGATCGTTTGCTATCTCCGAGGATAC
EST: gi|148964727|gb|EC905993.2|EC905993
EST:     TTGGTTGCTGACTATGTCGAAGTGGTCAGCAAGCACAATGATGATAAACA                         ATATGTTTGGGAATCAAAAGCTGATGGATCGTTTGCTATCTCCGAGG
genomic: TTGGTTGCTGACTATGTCGAAGTGGTCAGCAAGCACAATGATGATAAACAgtaagttacc ... actcttttagATATGTTTGGGAATCAAAAGCTGATGGATCGTTTGCTATCTCCGAGG
EST: gi|149112828|gb|EE295636.2|EE295636
EST:     TTGGTTGCTGACTATGTCGAAGTGGTCAGCAAGCACAATGATGATAAACA                         ATATGTTTGGGAATCAAAAGCTGATGGATCGT
genomic: TTGGTTGCTGACTATGTCGAAGTGGTCAGCAAGCACAATGATGATAAACAgtaagttacc ... actcttttagATATGTTTGGGAATCAAAAGCTGATGGATCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctcgttttacttatgtgcttgcctcacggtattttggtgctgtactcttttagATATGTTTGGGAATCAAAAGCTGATGGATCGTTTGCTATCTCCGAGGATACATGGAATGAACCCCTTGGCCGTGGAACCGAGATAAGATTACATCTGCGA
                      gcctcac  putative branch site (score: 3)
                                            tactctttt  putative PPT
      ttttacttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttaccgctgctgctttttttgttcatttctcgttttacttatgtgcttgcctcacggtattttggtgctgtactcttttagATATGTTTGGGAATCAAAAGCTGATGGATCGTTTGCTATCTCCGAGGATACATGGAATGAACCCCTTGGCCGTGGAACCGAGATAAGATTACATCTGCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA