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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtacttagcaatagcatgaaccctgtacttcatgttgcatgcttgtgtatcggttttgttagaaatttcagttgcatggtgaatattgctgtttcatctattaatggtctggttctagttgtttgtatctaaatgtacccttttgattttttatatccataggtccataacaacagcaaactcttatcacagGTTGAAGTGTTCCAGCGACAGCTCGAACTAGCTAAGGAATTGGAGAGACCTGTTTCTGTTCATTGTGTGCGGGCATTTGGTGATCTTCTGGAAGTATTGA

Basic information

species Zea mays
transcript GRMZM2G114131_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G114131_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os04g48820.2 (Oryza sativa), 3'ss of exon 4
gttagtacttagcaatagcatgaaccctgtacttcatgttgcatgcttgtgtatcggttttgttagaaatttcagttgcatggtgaatattgctgtttcatctattaatggtctggttctagttgttt-gtatctaaatgtacccttttgattttttatatccataggtccat-aacaacagcaaactcttatcacagGTTGAAGTGTTCCAGCGACAGCTCGAACTAGCTAAGGAATTGGAGAGACCTGTTTCTGTTCATTGTGTGCGGGCATTTGGTGATCTTCTGGAAGTATTGA
                                                                                        ||  ||    ||| ||       | ||  || |||  ||| | |||   |   | | || ||         | | ||| | | || |  | |   ||| | | |   ||||||||||| |||||||  || || ||||| |||||||| ||| | |  ||||||||||||||||||||||| || |||||||||||||||||  || | |
---------------------------------------------------------------------------------------aatcactaggccatataacc----tatgcctcaagtccttttgcatcatgagcaagctttatgcc-------accaataagactatcagaagctaaaaaatatcactgcagGTTGAAGTTTTCCAGCAGCAACTTGAACTTGCTAAGGAGTTGAACAAGCCTGTTTCTGTTCATTGTGTGCGCGCCTTTGGTGATCTTCTGGAGATACTAA

upper sequence: GRMZM2G114131_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT5G17570.1 (Arabidopsis thaliana), 3'ss of exon 4
gttagtacttagcaatagcatgaaccctgtacttcatgttgcatgcttgtgtatcggttttgttagaaatttcagttgcatggtgaatattgctgtttcatctattaatggtctggttctagttgtttgtatctaaatgtacccttttgattttttatatccataggtccataacaacagcaaactcttatcacagGTTGAAGTGTTCCAGCGACAGCTCGAACTAGCTAAGGAATTGGAGAGACCTGTTTCTGTTCATTGTGTGCGGGCATTTGGTGATCTTCTGGAAGTATTGA
                                                                                              ||||||   ||| |    | |           ||||   ||||||     | ||  |   | ||  |  | | | | |||  ||| ||   | | ||  ||||||   || || |  | |||||| ||||| || ||||||||| ||| |||||  || ||||||||||| || |||||||| ||||| || ||  |||| |
----------------------------------------------------------------------------------------------gtttcaga-attgaaaaacagacc--------ttgtggttaaatggtttatgttc-tcagtgatggcttttgatgc-taaagacatcat-ttttaatttcagGTTACCGTCTTTCGTCAACAGCTTGAACTTGCAAAGGAATTGAAGAAACCTGCGTCAGTTCATTGTGTTCGTGCATTTGGGGATCTACTCGAGATATTAA

upper sequence: GRMZM2G114131_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv15s0024g00050.t01 (Vitis vinifera), 3'ss of exon 5
gttagtacttagcaatagcatgaaccctgtacttcatgttgcatgcttgtgtatcggttttgttagaaatttcagttgcatggtgaatattgctgtttcatctattaatggtctggttctagttgtttgtatctaaatgtacccttttgattttttatatccataggtccataacaacagcaaactcttatcacagGTTGAAGTGTTCCAGCGACAGCTCGAACTAGCTAAGGAATTGGAGAGACCTGTTTCTGTTCATTGTGTGCGGGCATTTGGTGATCTTCTGGAAGTATTGA
                                                                                       |  | || |   |  |  |     |||| |  |||    |  ||   | ||||   | ||  |  | || | |  |   ||   | |       ||  |  | |  ||||||||||| ||||||| |||||| ||||| || || || ||| | ||||| |||||||| ||||| || || || ||||||||||||||  |  || || 
---------------------------------------------------------------------------------------tcctactctcctacttgct-----tctgataatag--aatgctaaagagatgttttccttgaagatgttttgtgaaacagtt--ttatttgtttaattttctgttccagGTTGAAGTTTTCCAGCAACAGCTTGAACTTGCCAAAGAGTTGAAAAGACCAGTTTCTGTCCATTGCGTTCGTGCTTTTGGTGATCTTCTTCAGATAATGC

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|148944967|gb|EC890137.2|EC890137
EST:     TTGGTCTGGACAAAGGTTCACATGGAAAAACCATCAACTTCGGAGAACAG                         GTGGAAGTGTTCCAGCGACAGCTCGAACTAGCTAAGGAATTGGAGAGACCT
genomic: TTGGTCTGGACAAAGGTTCACATGGAAAAACCATCAACTTCGGAGAACAGgttagtactt ... cttatcacagGTTGAAGTGTTCCAGCGACAGCTCGAACTAGCTAAGGAATTGGAGAGACCT
EST: gi|37417816|gb|CF646568.1|CF646568
EST:     TTGGTCTGGACAAAGGTTCACATGGAAAAACCATCAACTTCGGAGAACAG                         GTTGAAGTGTTCCAGCGACAGCTCGAACTAGCTAAGGAATTGGAGAGACCT
genomic: TTGGTCTGGACAAAGGTTCACATGGAAAAACCATCAACTTCGGAGAACAGgttagtactt ... cttatcacagGTTGAAGTGTTCCAGCGACAGCTCGAACTAGCTAAGGAATTGGAGAGACCT
EST: gi|60401013|gb|DN233820.1|DN233820
EST:     TTGGTCTGGACAAAGGTTCACATGGAAAAACCATCAACTTCGGAGAACAG                         GTTGAAGTGTTCCAGCGACAACTCGAACTAGCTAAGGAATTGGAGAGACCT
genomic: TTGGTCTGGACAAAGGTTCACATGGAAAAACCATCAACTTCGGAGAACAGgttagtactt ... cttatcacagGTTGAAGTGTTCCAGCGACAGCTCGAACTAGCTAAGGAATTGGAGAGACCT
EST: gi|50331796|gb|CO526922.1|CO526922
EST:     TTGGTCTGGACAAAGGTTCACATGGAAAAACCATCAACTTCGGAGAACAG                         GTTGAAGTGTTCCAGCGACAGCTCGAACTAGCTAAGGAATTGGAGAGACCT
genomic: TTGGTCTGGACAAAGGTTCACATGGAAAAACCATCAACTTCGGAGAACAGgttagtactt ... cttatcacagGTTGAAGTGTTCCAGCGACAGCTCGAACTAGCTAAGGAATTGGAGAGACCT
EST: gi|148944968|gb|EC890138.2|EC890138
EST:     TTGGTCTGGACAAAGGTTCACATGGAAAAACCATCAACTTCGGAGAACAG                         GTTGAAGTGTTCCAGCGACAGCTCGAACTAGCTAAGGAATTGGAGAGACCT
genomic: TTGGTCTGGACAAAGGTTCACATGGAAAAACCATCAACTTCGGAGAACAGgttagtactt ... cttatcacagGTTGAAGTGTTCCAGCGACAGCTCGAACTAGCTAAGGAATTGGAGAGACCT
EST: gi|78118988|gb|DV537372.1|DV537372
EST:     TTGGTCTGGACAAAGGTTCACATGGAAAAACCATCAACTTCGGAGAACAG                         GTTGAAGTGTTCCAGCGACAGCTCGAACTAGCTAAGGAATTGGAGAGACCT
genomic: TTGGTCTGGACAAAGGTTCACATGGAAAAACCATCAACTTCGGAGAACAGgttagtactt ... cttatcacagGTTGAAGTGTTCCAGCGACAGCTCGAACTAGCTAAGGAATTGGAGAGACCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccttttgattttttatatccataggtccataacaacagcaaactcttatcacagGTTGAAGTGTTCCAGCGACAGCTCGAACTAGCTAAGGAATTGGAGAGACCTGTTTCTGTTCATTGTGTGCGGGCATTTGGTGATCTTCTGGAAGTATTGA
                           ccataac  putative branch site (score: 3)
                                           ctcttatc  putative PPT
        attttttatatccata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtacttagcaatagcatgaaccctgtacttcatgttgcatgcttgtgtatcggttttgttagaaatttcagttgcatggtgaatattgctgtttcatctattaatggtctggttctagttgtttgtatctaaatgtacccttttgattttttatatccataggtccataacaacagcaaactcttatcacagGTTGAAGTGTTCCAGCGACAGCTCGAACTAGCTAAGGAATTGGAGAGACCTGTTTCTGTTCATTGTGTGCGGGCATTTGGTGATCTTCTGGAAGTATTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG