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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcaaattctctttgtttattcattaagtgcattattacattttaaaacatgacacttatttatgctactttctattttgatgcttctttccagACTTCTGATATCTTGTATTATGAGGTTCTGGACATTCCACTGCCAGAATTGCAGTGTTTGAAAACGCTTAAAGTTGCATTCCACCATGCAACAAAAGATG

Basic information

species Zea mays
transcript GRMZM2G014805_T01
intron # 23
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 23
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 23
gtcaaattctctttgtttattcattaagtgcattattacattttaaaacatgacacttatttatgctactttctattttgatgcttctttccagACTTCTGATATCTTGTATTATGAGGTTCTGGACATTCCACTGCCAGAATTGCAGTGTTTGAAAACGCTTAAAGTTGCATTCCACCATGCAACAAAAGATG
||  | |  ||||| |||      ||||  |     |||||     | |||    |||||  ||  || ||||     ||       ||| ||||||||||| ||||||||||| |||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||| |||||||
gtatattcttctttatttgcgacataagcac-----tacat----gaccattgggcttat--attttattttcacgcctggc----ttttgcagACTTCTGACATCTTGTATTACGAGGTTCTGGACATTCCACTGCCAGAATTGCAGTGTTTGAAAACTCTTAAAGTTGCATTCCACCATGCAACTAAAGATG

upper sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 23
lower sequence: GLYMA14G04890.1 (Glycine max), 3'ss of exon 23
gtcaaattctctttgtttattcattaagtgcattattacattttaaaacatgacacttatttatgctactttctattttgatgcttcttt-----ccagACTTCTGATATCTTGTATTATGAGGTTCTGGACATTCCACTGCCAGAATTGCAGTGTTTGAAAACGCTTAAAGTTGCATTCCACCATGCAACAAAAGATG
                      | | | ||  || |  ||  ||  | | ||   ||||||||    ||     || ||  | |||   |      |||||||| ||||| ||||| ||||| || || ||||| || ||||||||||| ||  | |||||||| || ||||||||||| ||||||||||| || ||||
--------------------gtaattattgacttgtcccaactttcatcttgtttcttatttaaaaaacaaaacatcttattcctttcatgcatgtcagACTTCGGATATATTGTACTATGAAGTACTTGACATCCCTCTGCCAGAATTACAAGGATTGAAAACTCTGAAAGTTGCATTTCACCATGCAACCAAGGATG

upper sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 23
lower sequence: GLYMA02G43930.1 (Glycine max), 3'ss of exon 23
gtcaaattctctttgtttattcattaagtgcattattacattttaaaacatgacacttatttatgctactttctattttgatgcttctttccagACTTCTGATATCTTGTATTATGAGGTTCTGGACATTCCACTGCCAGAATTGCAGTGTTTGAAAACGCTTAAAGTTGCATTCCACCATGCAACAAAAGATG
         |  || || | | |||  || || | || || | |      |   | |||   |     | | |||||    |  | | |  |||||||| ||||| ||||| ||||| || || ||||| || ||||||||| | ||  | |||||||| || ||||||||||| |||||||| || || ||||
--------gtaattattgacttatt--gtccaatctttcaatcttg--tttcttatttaaaaacaaagcatcctattcctttcatgcatgtcagACTTCGGATATATTGTACTATGAAGTACTTGACATCCCTCTGCCAGAACTACAAGGATTGAAAACTCTGAAAGTTGCATTTCACCATGCTACCAAGGATG

upper sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 23
lower sequence: AT5G06600.3 (Arabidopsis thaliana), 3'ss of exon 23
---------gtcaaattctctttg-tttattcattaagtgcattattacattttaaaacatgacacttatttatgctactttctattttgatgcttctttccagACTTCTGATATCTTGTATTATGAGGTTCTGGACATTCCACTGCCAGAATTGCAGTGTTTGAAAACGCTTAAAGTTGCATTCCACCATGCAACAAAAGATG
         || || |||    |  |||| | |||   ||  ||  || ||    ||| || | || | |     || |||  |  |||  |  || ||| ||||| ||||| || ||||||||||| ||||||||||| || || |||||||| ||  || | |||||  | |||||||| ||||| ||||| || || || |
gtaattgacgtgaagttcagcatactttacttatt---tgtcttgctatat----aaatataatacatgt-----ctgcttattggtttt-ttttttttttcagACGTCTGACATTTTGTATTATGAAGTTCTGGACATCCCTCTTCCAGAATTACAAGGTCTTAAAACCTTAAAAGTTGCTTTCCATCATGCCACGAAGGAAG

upper sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 23
lower sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 23
---------------------------------------------------gtcaaattctctttgtttattcat-taagtgcattattacattttaaaacatgacacttatttatgctactttctattttgatgcttctttccagACTTCTGATATCTTGTATTATGAGGTTCTGGACATTCCACTGCCAGAATTGCAGTGTTTGAAAACGCTTAAAGTTGCATTCCACCATGCAACAAAAGATG
                                                    |   ||| | ||| ||| || || ||  |  ||| ||| ||         | |||   | ||   || | ||||  ||||   |||     |||| ||||||||| || |||||||| ||||| ||||| || || |||||||||||  || ||||||  || |||||||| || || ||||| ||||| ||||
gttgctttcacaaatactgagacaaatttgatgcttgatatgatcgtttgttttttattttttttatttttttatatatatatatttttatataacttttagtaacagaaactt---cttccttcttctttggc-ctttggaacagAGTTCTGATATTTTATATTATGAAGTTCTAGACATCCCTCTTCCAGAATTGCAAGGTCTGAAAAATCTGAAAGTTGCTTTTCATCATGCTACAAAGGATG

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|32933255|gb|CF038067.1|CF038067
EST:     GATATAGGGGAGTAGAACATCTACTGGATATGCTTGTGCATTATAACCAG                         ACTTCTGATATCTTGTATTATGAGGTTCTGGACATTCCACTGCCAGAATTG
genomic: GATATAGGGGAGTAGAACATCTACTGGATATGCTTGTGCATTATAACCAGgtcaaattct ... ttctttccagACTTCTGATATCTTGTATTATGAGGTTCTGGACATTCCACTGCCAGAATTG
EST: gi|32934023|gb|CF038835.1|CF038835
EST:     GATATAGGGGAGTAGAACATCTACTGGATATGCTTGTGCATTATAACCAG                         ACTTCTGATATCTTGTATTATGAGGTTCTGGACATTCCACTGCCAGAATTG
genomic: GATATAGGGGAGTAGAACATCTACTGGATATGCTTGTGCATTATAACCAGgtcaaattct ... ttctttccagACTTCTGATATCTTGTATTATGAGGTTCTGGACATTCCACTGCCAGAATTG
EST: gi|60354119|gb|DN221092.1|DN221092
EST:     GATATAGGGGAGTAGAACATCTACTGGATATGCTTGTGCATTATAACCAG                         ACTTCTGATATCTTGTATTATGAGGTTCTGGACATTCCACTGCCAGAATTG
genomic: GATATAGGGGAGTAGAACATCTACTGGATATGCTTGTGCATTATAACCAGgtcaaattct ... ttctttccagACTTCTGATATCTTGTATTATGAGGTTCTGGACATTCCACTGCCAGAATTG
EST: gi|76019060|gb|DT946230.1|DT946230
EST:     GATATAGGGGAGTAGAACATCTACTGGATATGCTTGTGCATTATAACCAG                         ACTTCTGATATCTTGTATTATGAGGTTCTGGACATTCCACTGCCAGAATTG
genomic: GATATAGGGGAGTAGAACATCTACTGGATATGCTTGTGCATTATAACCAGgtcaaattct ... ttctttccagACTTCTGATATCTTGTATTATGAGGTTCTGGACATTCCACTGCCAGAATTG
EST: gi|13178629|gb|BG349887.1|BG349887
EST:     GATATAGGGGAGTAGAACATCTACTGGATATGCTTGTGCATTATAACCAG                         ACTTCTGATATCTTGTATTATGAGGTTTTGGTCTTTCCACTGCCAGAATTG
genomic: GATATAGGGGAGTAGAACATCTACTGGATATGCTTGTGCATTATAACCAGgtcaaattct ... ttctttccagACTTCTGATATCTTGTATTATGAGGTTCTGGACATTCCACTGCCAGAATTG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 212

GCTTACATCTCACAATTGTTATTCTCAGCAACCTAAACCACAACCTATTAGATATAGGGGAGTAGAACATCTACTGGATATGCTTGTGCATTATAACCAGgtcaaattct ... ttctttccagACTTCTGATATCTTGTATTATGAGGTTCTGGACATTCCACTGCCAGAATTGCAGTGTTTGAAAACGCTTAAAGTTGCATTCCACCATGCAACAAAAGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 222

GCTTACATCTCACAATTGTTATTCTCAGCAACCTAAACCACAACCTATTAGATATAGGGGAGTAGAACATCTACTGGATATGCTTGTGCATTATAACCAGgtcaaattct ... ttctttccagACTTCTGATATCTTGTATTATGAGGTTCTGGACATTCCACTGCCAGAATTGCAGTGTTTGAAAACGCTTAAAGTTGCATTCCACCATGCAACAAAAGATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 221

GCTTACATCTCACAATTGTTATTCTCAGCAACCTAAACCACAACCTATTAGATATAGGGGAGTAGAACATCTACTGGATATGCTTGTGCATTATAACCAGgtcaaattct ... ttctttccagACTTCTGATATCTTGTATTATGAGGTTCTGGACATTCCACTGCCAGAATTGCAGTGTTTGAAAACGCTTAAAGTTGCATTCCACCATGCAACAAAAGATG


Block sizes: 44 (upstream exon), 47 (downstream exon)
Score: 170

GCTTACATCTCACAATTGTTATTCTCAGCAACCTAAACCACAACCTATTAGATATAGGGGAGTAGAACATCTACTGGATATGCTTGTGCATTATAACCAGgtcaaattct ... ttctttccagACTTCTGATATCTTGTATTATGAGGTTCTGGACATTCCACTGCCAGAATTGCAGTGTTTGAAAACGCTTAAAGTTGCATTCCACCATGCAACAAAAGATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttaaaacatgacacttatttatgctactttctattttgatgcttctttccagACTTCTGATATCTTGTATTATGAGGTTCTGGACATTCCACTGCCAGAATTGCAGTGTTTGAAAACGCTTAAAGTTGCATTCCACCATGCAACAAAAGATG
                                    ttttgat  putative branch site (score: 170)
                                          tgcttctttcc  CT-rich tract
               acttatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcaaattctctttgtttattcattaagtgcattattacattttaaaacatgacacttatttatgctactttctattttgatgcttctttccagACTTCTGATATCTTGTATTATGAGGTTCTGGACATTCCACTGCCAGAATTGCAGTGTTTGAAAACGCTTAAAGTTGCATTCCACCATGCAACAAAAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG