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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatttttaatgttagcttactcgtattatggaaattgaaaaaaacatttattttgcacgtgacattctttattttgtccgatgttttgattgcaaaacagGAATTCAGTGACCCCCGTGATGCTGATGATGCGCAGTACAACCTAGATGGCAGGGAAGTCGATGGAAGCCGTATTATTGTTGAATTTGCTAAAGGA

Basic information

species Zea mays
transcript GRMZM2G099186_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G099186_T03 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA03G33270.1 (Glycine max), 3'ss of exon 3
---------------------------------------------------------gatttttaatgttagcttactcgtattatggaaattgaaaaaaacatttattt-tgcacgtgacattct---ttattttgtccgatgttt--tgat---tgcaaaacagGAATTCAGTGACCCCCGTGATGCTGATGATGCGCAGTACAACCTAGATGGCAGGGAAGTCGATGGAAGCCGTATTATTGTTGAATTTGCTAAAGGA
                                                             |||  |   || |  ||  || |||       ||  ||  || || |   || | || | ||||    ||| ||| |  | |  ||  |||    |    |||||||||| ||||| || || ||||||||||||||    |||||||| |||||  | || || || ||||| ||||||||||| |||||||| || || 
gtaagttgtcaccctttctgtctttatgtatttcttttttacttcaatttctcctcatgcctttgctccaaggtggcttttagtatctgctcggaggaattcagttgtaaatgaaggtaagattcggtgttactttattggcttgttcctgacatattttgaacagGAATTTAGTGATCCTCGAGATGCTGATGATGCTAGATACAACCTGGATGGTCGTGATGTTGAAGGAAGTCGTATTATTGTGGAATTTGCCAAGGGG

upper sequence: GRMZM2G099186_T03 (Zea mays), 3'ss of exon 4
lower sequence: Vv08s0040g02860.t01 (Vitis vinifera), 3'ss of exon 1
--------------------------------------------------------------gatttttaatgttagcttactcgtattatggaaattgaaaaaaacatttattttgcacgtgacattctttattttgtccgatgttttgattgcaaaacagGAATTCAGTGACCCCCGTGATGCTGATGATGCGCAGTACAACCTAGATGGCAGGGAAGTCGATGGAAGCCGTATTATTGTTGAATTTGCTAAAGGA
                                                              |  ||||  |  |   |||    ||  |   | |||  | |     ||        | | |     | || ||   ||      ||   ||     ||||||||||||||| ||||| ||||||||||||||    || ||| || ||||  | ||  | |||||||| ||||| ||||| |||||||| ||||| 
gtatgtatcaaccatttgttcatctatttctttcctttttctcccttgcttatggttatggagtatttttctccttatttatctatagaagtcacattatagatggtgttacacaaatatgagcatcccgttgttcgttcttgcacttaattttatctacagGAATTCAGTGATCCCCGAGATGCTGATGATGCAAGATATAACTTAAATGGACGAGATTTTGATGGAAGTCGTATCATTGTGGAATTTGCGAAAGGG
















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|6431785|gb|AW171989.1|AW171989
EST:     CGTGACTATGCATTCATT                         GAATTCAGTGACCCCCGTGATGCTGATGATGCGCAGTACAACCTAGATGGC
genomic: CGTGACTATGCATTCATTgtatgttcta ... tgcaaaacagGAATTCAGTGACCCCCGTGATGCTGATGATGCGCAGTACAACCTAGATGGC
EST: gi|19057891|gb|BM736558.1|BM736558
EST:     GAGTTGAAGCGTGACTATGCATTCATT                         GAATTCAGTGACCCCCGTGATGCTGATGATGCGCAGTACAACCTAGATGGC
genomic: GAGTTGAAGCGTGACTATGCATTCATTgtatgttcta ... tgcaaaacagGAATTCAGTGACCCCCGTGATGCTGATGATGCGCAGTACAACCTAGATGGC
EST: gi|71309062|gb|DR790796.1|DR790796
EST:     AATACGTGAAGTGGAGTTGAAGCGTGACTATGCATTCATT                         GAATTCAGTGACCCCCGTGATGCTGATGATGCGCAGTACAACCTAGATGGC
genomic: AATACGTGAAGTGGAGTTGAAGCGTGACTATGCATTCATTgtatgttcta ... tgcaaaacagGAATTCAGTGACCCCCGTGATGCTGATGATGCGCAGTACAACCTAGATGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttattttgcacgtgacattctttattttgtccgatgttttgattgcaaaacagGAATTCAGTGACCCCCGTGATGCTGATGATGCGCAGTACAACCTAGATGGCAGGGAAGTCGATGGAAGCCGTATTATTGTTGAATTTGCTAAAGGA
                                      ttttgat  putative branch site (score: 4)
                acattctttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatttttaatgttagcttactcgtattatggaaattgaaaaaaacatttattttgcacgtgacattctttattttgtccgatgttttgattgcaaaacagGAATTCAGTGACCCCCGTGATGCTGATGATGCGCAGTACAACCTAGATGGCAGGGAAGTCGATGGAAGCCGTATTATTGTTGAATTTGCTAAAGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG