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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgaatgttttcttgtttgaagctaagtcagtcatgcatacacaattgacaagttgtaaaaggactgaagatgtttacatattgtttttttaatcttgcagAGAGATGATTCAGCACAGGCCATATGACCAAAAAGTTGATGTCTACAGCTTTGGCATTGTGCTGTGGGAGCTCATAACTGGCATGCTCCCTTTTGCTAAT

Basic information

species Zea mays
transcript GRMZM2G102088_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G102088_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os04g51950.1 (Oryza sativa), 3'ss of exon 2
cgaatgttttcttgtttgaagcta-agtcagtcatgcatacacaattgacaagttgtaaaag-gactgaagatgtttacatattgtttttttaatcttgcagAGAGATGATTCAGCACAGGCCATATGACCAAAAAGTTGATGTCTACAGCTTTGGCATTGTGCTGTGGGAGCTCATAACTGGCATGCTCCCTTTTGCTAAT
 || |  |||  | |||   | |  |    || || | | ||  |    ||  || | ||   |  |   ||||| |  |      | |||| ||| |||||||| |||||||||||||||||||||||||| ||||| |||||||| |||||||||||||| || ||||||||||| ||||||||||||||||| ||||| 
-gagttgttttctatttactgtttcaaattgtaattcgttcaatacattcatcttattaacttggttcctgatgtctg-actcgcctattttgatcctgcagAGAAATGATTCAGCACAGGCCATATGACCAGAAAGTAGATGTCTATAGCTTTGGCATTGTTCTATGGGAGCTCATTACTGGCATGCTCCCTTTCGCTAAC

upper sequence: GRMZM2G102088_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv04s0008g03020.t01 (Vitis vinifera), 3'ss of exon 2
---cgaatgttttcttgtttgaagctaagtcagtcatgcatacacaattgacaagttgtaaaaggactgaagatgtttacatattgtttttttaatcttgcagAGAGATGATTCAGCACAGGCCATATGACCAAAAAGTTGATGTCTACAGCTTTGGCATTGTGCTGTGGGAGCTCATAACTGGCATGCTCCCTTTTGCTAAT
     ||      |   ||  ||  |  ||     || | |  | | || | ||||  |  |  |  |   ||| |||  || | |  ||  |  ||||||||||||||||| ||||||||||||||    || || || ||||||||||||||||| ||||| |||||||||||||| || ||| |||| || ||    || 
catgaaacaggaccaccttgtaatttttgttgtagattcttttatattt-ataagtgattcattggtttt-gattttttgatgt-gcgttacttttcttgcagAGAGATGATCCAGCACAGGCCATACACTCAGAAGGTAGATGTCTACAGCTTTGGAATTGTCCTGTGGGAGCTCATCACAGGCTTGCTTCCCTTCCAGAAC

upper sequence: GRMZM2G102088_T02 (Zea mays), 3'ss of exon 2
lower sequence: EFJ13809 (Selaginella moellendorffii), 3'ss of exon 1
cgaatgttttcttgtttgaagctaagtcagtcatgcatacaca-attgacaagttgtaaaaggactgaagatgtttacatattgtttttttaatcttgcagAGAGATGATTCAGCACAGGCCATATGACCAAAAAGTTGATGTCTACAGCTTTGGCATTGTGCTGTGGGAGCTCATAACTGGCATGCTCCCTTTTGCTAAT
     ||   |   |||    ||  ||       || |   |   ||         ||    ||||  | |   | ||  |  ||||  || ||  |||||||||||||| ||||||||||  ||    || || || || || |||||||||||||||||||||||||||||||| || ||  |||| || ||    || 
-----gtaagcgcatttctctcttcgttctcttcgcgttttcgtgttcttcctccatagctagacttcaaagcctcactaaccgtttcattcat--tgcagAGAGATGATCCAGCACAGGCTTTACACGCACAAGGTGGACGTTTACAGCTTTGGCATTGTGCTGTGGGAGCTCATCACAGGATTGCTACCGTTCCAGAAC

upper sequence: GRMZM2G102088_T02 (Zea mays), 3'ss of exon 2
lower sequence: EFJ28993 (Selaginella moellendorffii), 3'ss of exon 1
cgaatgttttcttgtttgaagctaagtcagtcatgcatacaca-attgacaagttgtaaaaggactgaagatgtttacatattgtttttttaatcttgcagAGAGATGATTCAGCACAGGCCATATGACCAAAAAGTTGATGTCTACAGCTTTGGCATTGTGCTGTGGGAGCTCATAACTGGCATGCTCCCTTTTGCTAAT
     ||   |   |||    ||  ||       || |   |   ||         ||    ||||  | |   | ||  |  ||||  || ||  |||||||||||||| ||||||||||  ||    || || || || || ||||||||||||||||| |||||||||||||| || ||  |||| || ||    || 
-----gtaagcgcatttctctcttcgttctcttcgcgttttcgtgttcttcctccatagctagacttcaaagcctcactaaccgtttcattcat--tgcagAGAGATGATCCAGCACAGGCTTTACACACACAAGGTGGACGTTTACAGCTTTGGCATTGTCCTGTGGGAGCTCATCACAGGATTGCTACCGTTCCAGAAC

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|148982646|gb|EE028447.2|EE028447
EST:     AAAACTGAGGGGATGACACCTGAAACGGGAACCTATCGTTGGATGGCACC                         AGAGATGATTCAGCACAGGCCATATGACCAAAAAGTTGATGTCTACAGCTT
genomic: AAAACTGAGGGGATGACACCTGAAACGGGAACCTATCGTTGGATGGCACCgtaagttgaa ... aatcttgcagAGAGATGATTCAGCACAGGCCATATGACCAAAAAGTTGATGTCTACAGCTT
EST: gi|71762094|gb|DR960031.1|DR960031
EST:     AAAACTGAGGGGATGACACCTGAAACGGGAACCTATCGTTGGATGGCACC                         AGAGATGATTCAGCACAGGCCATATGACCAAAAAGTTGATGTCTACAGCTT
genomic: AAAACTGAGGGGATGACACCTGAAACGGGAACCTATCGTTGGATGGCACCgtaagttgaa ... aatcttgcagAGAGATGATTCAGCACAGGCCATATGACCAAAAAGTTGATGTCTACAGCTT
EST: gi|116819043|gb|EC862128.1|EC862128
EST:     AAAACTGAGGGGATGACACCTGAAACGGGAACCTATCGTTGGATGGCACC                         AGAGATGATTCAGCACAGGCCATATGACCAAAAAGTTGATGTCTACAGCTT
genomic: AAAACTGAGGGGATGACACCTGAAACGGGAACCTATCGTTGGATGGCACCgtaagttgaa ... aatcttgcagAGAGATGATTCAGCACAGGCCATATGACCAAAAAGTTGATGTCTACAGCTT
EST: gi|31361978|gb|CD446335.1|CD446335
EST:     AAAACTGAGGGGATGACACTTGAAACGGGAACCTATCGTTGGATGGCACC                         AGAGATGATTCAGCACAGGCCATATGACCAAAAAGTTGATGTCTACAGCTT
genomic: AAAACTGAGGGGATGACACCTGAAACGGGAACCTATCGTTGGATGGCACCgtaagttgaa ... aatcttgcagAGAGATGATTCAGCACAGGCCATATGACCAAAAAGTTGATGTCTACAGCTT
EST: gi|6012220|gb|AW061762.1|AW061762
EST:     AAAACTGAGGGGATGACACCTGAAACGGGAACCTACCGTTGGATGGCACC                         AGAGATGATTCAGCACAGGCCATATGACCAAAAAGTTGATGTCTACAGCTT
genomic: AAAACTGAGGGGATGACACCTGAAACGGGAACCTATCGTTGGATGGCACCgtaagttgaa ... aatcttgcagAGAGATGATTCAGCACAGGCCATATGACCAAAAAGTTGATGTCTACAGCTT
EST: gi|47962131|gb|CN844840.1|CN844840
EST:     AAAACTGAGGGGATGACACCTGAAACGGGAACCTATCGTTGGATGGCACC                         AGAGATGATTCAGTACAGGCCATATGACCAAAAAGTTGATGTCTACAGCTT
genomic: AAAACTGAGGGGATGACACCTGAAACGGGAACCTATCGTTGGATGGCACCgtaagttgaa ... aatcttgcagAGAGATGATTCAGCACAGGCCATATGACCAAAAAGTTGATGTCTACAGCTT
EST: gi|211219776|gb|FL407448.1|FL407448
EST:     AAAACTGAGGGGATGACACCTGAAACGGGAACCTATCGTTGGATGGCACC                         AGAGATGATTCAGCACAGGCCATATGACCAAAAAGTTGATGTCTACAGCTT
genomic: AAAACTGAGGGGATGACACCTGAAACGGGAACCTATCGTTGGATGGCACCgtaagttgaa ... aatcttgcagAGAGATGATTCAGCACAGGCCATATGACCAAAAAGTTGATGTCTACAGCTT
EST: gi|32866602|gb|CF006284.1|CF006284
EST:     AAAACTGAGGGGATGACACCTGAAACGGGAACCTATCGTTGGATGGCACC                         AGAGATGATTCAGCACAGGCCATATGACCAAAAAGTTGATGTCTACAGTTT
genomic: AAAACTGAGGGGATGACACCTGAAACGGGAACCTATCGTTGGATGGCACCgtaagttgaa ... aatcttgcagAGAGATGATTCAGCACAGGCCATATGACCAAAAAGTTGATGTCTACAGCTT
EST: gi|32850190|gb|CD989871.1|CD989871
EST:     AAAACTGAGGGGATGACACCTGAAACGGGAACCTATCGTTGGATGGCACC                         AGAGATGATTCAGCACAGGCCATATGACCAAAAAGTTGATGTCTACAGTTT
genomic: AAAACTGAGGGGATGACACCTGAAACGGGAACCTATCGTTGGATGGCACCgtaagttgaa ... aatcttgcagAGAGATGATTCAGCACAGGCCATATGACCAAAAAGTTGATGTCTACAGCTT
EST: gi|44681913|gb|CK786961.1|CK786961
EST:     AAAACTGAGGGGATGACACCTGAAACGGGAACCTATCGTTGGATGGCACC                         AGAGATGATTCAGCACGGGGCCATATGACCAAAAAGTTGATGTCTACAGCT
genomic: AAAACTGAGGGGATGACACCTGAAACGGGAACCTATCGTTGGATGGCACCgtaagttgaa ... aatcttgcagAGAGATGATTCAGCACAGG-CCATATGACCAAAAAGTTGATGTCTACAGCT
EST: gi|32945076|gb|CF049895.1|CF049895
EST:     AAAACTGAGGGGATGACACCTGAAACGGGAACCTATCGTTGGATGGCACC                         AGAGATGATTCAGCACAGGCCATATG
genomic: AAAACTGAGGGGATGACACCTGAAACGGGAACCTATCGTTGGATGGCACCgtaagttgaa ... aatcttgcagAGAGATGATTCAGCACAGGCCATATG
EST: gi|32866890|gb|CF006572.1|CF006572
EST:     AAAACTGAGGGGATGACACCTGAAACGGGAACCTATCGTTGGATGGCACC                         AGAGATGATTCAGCACAGGCCATATGACCAAAAAGTTGATGTCTACAGTTT
genomic: AAAACTGAGGGGATGACACCTGAAACGGGAACCTATCGTTGGATGGCACCgtaagttgaa ... aatcttgcagAGAGATGATTCAGCACAGGCCATATGACCAAAAAGTTGATGTCTACAGCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgacaagttgtaaaaggactgaagatgtttacatattgtttttttaatcttgcagAGAGATGATTCAGCACAGGCCATATGACCAAAAAGTTGATGTCTACAGCTTTGGCATTGTGCTGTGGGAGCTCATAACTGGCATGCTCCCTTTTGCTAAT
                                         ttttaat  putative branch site (score: 3)
                                      ttttttta  CT-rich tract
                     aagatgtttacatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgaatgttttcttgtttgaagctaagtcagtcatgcatacacaattgacaagttgtaaaaggactgaagatgtttacatattgtttttttaatcttgcagAGAGATGATTCAGCACAGGCCATATGACCAAAAAGTTGATGTCTACAGCTTTGGCATTGTGCTGTGGGAGCTCATAACTGGCATGCTCCCTTTTGCTAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA