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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaactgaagttaaatagcatatcataaataatgccataatcgccaatgttgctcagagtaacttctgtgttctgacccttcttggtcctatacttcagGAATTTGACTACACCGAGTTAGATGAAGTGACAGAGTATTACCCACAATTTTATCATGGAGTAGATAAAGAGGGAAGACCTGTCTACATAGAATTAGTAG

Basic information

species Zea mays
transcript GRMZM2G174990_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174990_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g46720.2 (Oryza sativa), 3'ss of exon 3
gtaaaactgaagttaaatagcatatcataaataatgccataatcgccaatgttgctcagagtaacttctgtgttctgacccttcttggtcctatacttcagGAATTTGACTACACCGAGTTAGATGAAGTGACAGAGTATTACCCACAATTTTATCATGGAGTAGATAAAGAGGGAAGACCTGTCTACATAGAATTAGTAG
                        | | |  |   |    |    |  || |     | |    |   | | |  |||| ||| ||  |||| |   |||||| |||||||||||||||   ||||| || |   | ||||| ||||||||||| |||||||| |||||||| ||||| ||| |||||||||| ||| |||
-----------------------gtaaaaggttgcgttgaagaaacatatctaatataaatatgccattctatcatgacacttgtttatcctttctctcagGAGTTTGACTACACCGAGGCGGATGAGGTTATGAAATATTATCCACAATTTTACCATGGAGTGGATAAAGAAGGAAGGCCTATCTACATAGAGTTAATAG
















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|101402477|gb|EB822801.1|EB822801
EST:     GGTCAGACATGATCAATTGGAGGAAGGAATTCGGAGTCGACAAAATAGAG                         GAATTTGACTACACCGA
genomic: GGTCAGACATGATCAATTGGAGGAAGGAATTCGGAGTCGACAAAATAGAGgtaaaactga ... tatacttcagGAATTTGACTACACCGA
EST: gi|211480226|gb|FK977831.1|FK977831
EST:     GGTCAGACATGATCAATTGGAGGAAGGAATTCGGAGTCGACAAAATAGAG                         GAATTTGACTACACCGAGTTAGATGAAGTGACAGAGTATTACCCACAATTT
genomic: GGTCAGACATGATCAATTGGAGGAAGGAATTCGGAGTCGACAAAATAGAGgtaaaactga ... tatacttcagGAATTTGACTACACCGAGTTAGATGAAGTGACAGAGTATTACCCACAATTT
EST: gi|31353713|gb|CD438070.1|CD438070
EST:     GGTCAGACATGATCAATTGGAGGAAGGAATTCGGAGTCGACAAAATAGAG                         GATTTTGACTACACCGAGTTAGATGAAGTGACAGAGTATTACCCACAATTT
genomic: GGTCAGACATGATCAATTGGAGGAAGGAATTCGGAGTCGACAAAATAGAGgtaaaactga ... tatacttcagGAATTTGACTACACCGAGTTAGATGAAGTGACAGAGTATTACCCACAATTT
EST: gi|60338296|gb|DN205269.1|DN205269
EST:     GGTCAGACATGATCAATTGGAGGAAGGAATTCGGAGTCGACAAAATAGAG                         GAATTTGACTACACCGAGTTAGATGAAGTGACAGAGTATTACCCACAATTT
genomic: GGTCAGACATGATCAATTGGAGGAAGGAATTCGGAGTCGACAAAATAGAGgtaaaactga ... tatacttcagGAATTTGACTACACCGAGTTAGATGAAGTGACAGAGTATTACCCACAATTT
EST: gi|211483110|gb|FK977837.1|FK977837
EST:     GGTCAGACATGATCAATTGGAGGAAGGAATTCGGAGTCGACAAAATAGAG                         GAATTTGACTACACCGAGTTAGATGAAGTGACAGAGTATTACCCACAATTT
genomic: GGTCAGACATGATCAATTGGAGGAAGGAATTCGGAGTCGACAAAATAGAGgtaaaactga ... tatacttcagGAATTTGACTACACCGAGTTAGATGAAGTGACAGAGTATTACCCACAATTT
EST: gi|31997893|gb|CD661823.1|CD661823
EST:     GGTCAGACATGATCAATTGGAGGAAGGAATTCGGAGTCGACAAAATAGAG                         GAATTTGACTACACCGAGTTAGATGAAGTGACAGAGTATTACCCACAATTT
genomic: GGTCAGACATGATCAATTGGAGGAAGGAATTCGGAGTCGACAAAATAGAGgtaaaactga ... tatacttcagGAATTTGACTACACCGAGTTAGATGAAGTGACAGAGTATTACCCACAATTT
EST: gi|211480225|gb|FK977830.1|FK977830
EST:     GGCCAGACATGATCAATTGGNGGAAGGAATTCGGAGTCGACAAAATAGAG                         GAATTTGACTA
genomic: GGTCAGACATGATCAATTGGAGGAAGGAATTCGGAGTCGACAAAATAGAGgtaaaactga ... tatacttcagGAATTTGACTA
EST: gi|149084713|gb|EE174205.2|EE174205
EST:     GGTCAGACATGATCAATTGGAGGAAGGAATTCGGAGTCGACAAAATAGAG                         GAATTTGACTACACCGAGTTAGATGAAGTGACAGAGTATTACCCACAATTT
genomic: GGTCAGACATGATCAATTGGAGGAAGGAATTCGGAGTCGACAAAATAGAGgtaaaactga ... tatacttcagGAATTTGACTACACCGAGTTAGATGAAGTGACAGAGTATTACCCACAATTT
EST: gi|211483108|gb|FK977835.1|FK977835
EST:     GGTCAGACATGATCAATTGGAGGAAGGAATTCGGGGTCGACAAAATAGAA                         GAATTTGACTACACCGAGTTAGATGAAGTGACAGAGTATTACCCCACAATT
genomic: GGTCAGACATGATCAATTGGAGGAAGGAATTCGGAGTCGACAAAATAGAGgtaaaactga ... tatacttcagGAATTTGACTACACCGAGTTAGATGAAGTGACAGAGTATTACCC-ACAATT
EST: gi|71426247|gb|DR807297.1|DR807297
EST:     GGTCAGACATGATCAATTGGAGGAAGGAATTCGGAGTCGACAAAATAGAG                         GAATTTGACTACACCGAGTTAGATGAAGTGACAGAGTATTACCCACAATTT
genomic: GGTCAGACATGATCAATTGGAGGAAGGAATTCGGAGTCGACAAAATAGAGgtaaaactga ... tatacttcagGAATTTGACTACACCGAGTTAGATGAAGTGACAGAGTATTACCCACAATTT
EST: gi|211480223|gb|FK977828.1|FK977828
EST:     GGTCAGACATGATCAATTGGAGGAAGGAATTCGGAGTCGACAAAATAGAG                         GAATTTGACTACACCGAGTTAGATGAAGTGACAGAGTATTACCCACAATTT
genomic: GGTCAGACATGATCAATTGGAGGAAGGAATTCGGAGTCGACAAAATAGAGgtaaaactga ... tatacttcagGAATTTGACTACACCGAGTTAGATGAAGTGACAGAGTATTACCCACAATTT
EST: gi|28931255|gb|CB334616.1|CB334616
EST:     GGTCAGACATGATCAATTGGAGGAAGGAATTCGGAGTCGACAAAATAGAG                         GAATTTGACTACACCGAGTTAGATGAAGTGACAGAGTATTACCCACAATTT
genomic: GGTCAGACATGATCAATTGGAGGAAGGAATTCGGAGTCGACAAAATAGAGgtaaaactga ... tatacttcagGAATTTGACTACACCGAGTTAGATGAAGTGACAGAGTATTACCCACAATTT
EST: gi|211480220|gb|FK977825.1|FK977825
EST:     GGTCAGACATGATCAATTGGAGGAAGGAATTCGGAGTCGACAAAATAGAG                         GAATTTGACTACNCCGAGTTAGATGAAGTGACAGAGTATTACCCACAATTT
genomic: GGTCAGACATGATCAATTGGAGGAAGGAATTCGGAGTCGACAAAATAGAGgtaaaactga ... tatacttcagGAATTTGACTACACCGAGTTAGATGAAGTGACAGAGTATTACCCACAATTT
EST: gi|60351666|gb|DN218639.1|DN218639
EST:     GGTCAGACATGATCAATTGGAGGAAGGAATTCGGAGTCGACAAAATAGAG                         GAATTTGACTACACCGAGTTAGATGAAGTGACAGAGTATTACCCACAATTT
genomic: GGTCAGACATGATCAATTGGAGGAAGGAATTCGGAGTCGACAAAATAGAGgtaaaactga ... tatacttcagGAATTTGACTACACCGAGTTAGATGAAGTGACAGAGTATTACCCACAATTT
EST: gi|211483114|gb|FK977841.1|FK977841
EST:     GGTCAGACATGATCAATTGGAGGAAGGAATTCGGAGTCGACAAAATAGAG                         GAATTTGACTACACCGAGTTAGATGAAGTGACAGAGTATTACCCACAATTT
genomic: GGTCAGACATGATCAATTGGAGGAAGGAATTCGGAGTCGACAAAATAGAGgtaaaactga ... tatacttcagGAATTTGACTACACCGAGTTAGATGAAGTGACAGAGTATTACCCACAATTT
EST: gi|101386148|gb|EB815117.1|EB815117
EST:     GGTCAGACATGATCAATTGGAGGAAGGAATTCGGAGTCGACAAAATAGAG                         GAATTTGACTACACCGAGTTAGATGAAGTGACAGAGTATTACCCACAATTT
genomic: GGTCAGACATGATCAATTGGAGGAAGGAATTCGGAGTCGACAAAATAGAGgtaaaactga ... tatacttcagGAATTTGACTACACCGAGTTAGATGAAGTGACAGAGTATTACCCACAATTT
EST: gi|31611997|gb|CD568619.1|CD568619
EST:     GGTCAGACATGATCAATTGGAGGAAGGAATTCGGAGTCGACAAAATAGAG                         GAATTTGACTACACCGAGTTAGATGAAGTGACAGAGTATTACCCACAATTT
genomic: GGTCAGACATGATCAATTGGAGGAAGGAATTCGGAGTCGACAAAATAGAGgtaaaactga ... tatacttcagGAATTTGACTACACCGAGTTAGATGAAGTGACAGAGTATTACCCACAATTT
EST: gi|211480224|gb|FK977829.1|FK977829
EST:     GGTCAGACATGATCAATTGGAGGAAGGAATTCGGAGTCGACAAAATAGAG                         GAATTTGACTACACCGAGTTAGATGAAGTGACAGAGTATTACCCACAATTT
genomic: GGTCAGACATGATCAATTGGAGGAAGGAATTCGGAGTCGACAAAATAGAGgtaaaactga ... tatacttcagGAATTTGACTACACCGAGTTAGATGAAGTGACAGAGTATTACCCACAATTT
EST: gi|211483113|gb|FK977840.1|FK977840
EST:     GGTCAGACATGATCAATTGGAGGAAGGAATTCGGAGTCGACAAAATAGAG                         GAATTTGACTACNCCGAGTTAGATGAAGTGACAGAGTATTACCCACAATTT
genomic: GGTCAGACATGATCAATTGGAGGAAGGAATTCGGAGTCGACAAAATAGAGgtaaaactga ... tatacttcagGAATTTGACTACACCGAGTTAGATGAAGTGACAGAGTATTACCCACAATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatgttgctcagagtaacttctgtgttctgacccttcttggtcctatacttcagGAATTTGACTACACCGAGTTAGATGAAGTGACAGAGTATTACCCACAATTTTATCATGGAGTAGATAAAGAGGGAAGACCTGTCTACATAGAATTAGTAG
                          ttctgac  putative branch site (score: 2)
                                cccttcttggtcct  CT-rich tract
                                             tatactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaactgaagttaaatagcatatcataaataatgccataatcgccaatgttgctcagagtaacttctgtgttctgacccttcttggtcctatacttcagGAATTTGACTACACCGAGTTAGATGAAGTGACAGAGTATTACCCACAATTTTATCATGGAGTAGATAAAGAGGGAAGACCTGTCTACATAGAATTAGTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA