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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgacgcgaacgaacactagtgcgacagttatatatacgtactactacgtacagtctagcttcaccgtctgacatgcatgagagatgacttttcttcttcttttttttctcccccttcttcttccactccatagGAGGACATGATCATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTGATGAAGTTCAA

Basic information

species Zea mays
transcript GRMZM2G122172_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G122172_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os06g39230.1 (Oryza sativa), 3'ss of exon 6
gtgcgacgcgaacgaacactagtgcgacagttatatatacgtactactacgtacagtctagcttcaccgtctgacatgcatgagagatgacttttct---tcttcttttttttctcccccttcttcttccactccatagGAGGACATGATCATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTGATGAAGTTCAA
                                     ||   | ||  |  || | |  | ||| |   | |  || | |      |||  | |||    |||| | | |  |    | |||    |||    | | |||| |||||| |||| |||| ||||||||||||||| ||||||||||||||||||||||||||
------------------------------------gtaaaga-taaaaaata-aattaacctttagaatttaccacgaacacaccatgtgtcttcacagtcttatctctgatgattcgcttgcgattctgaacgacagGACGACATGGTCATCGCGAGGGAGGAGATCTTCGGCCCCGTCATGTGCCTGATGAAGTTCAA
















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|5005600|gb|AI711662.1|AI711662
EST:     CGGAAGGGAAAGGCTACTACATTGAGCCCACAGTTTTCACCAACGTCAAG                         GAGGACATGATCATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTG
genomic: CGGAAGGGAAAGGCTACTACATTGAGCCCACAGTTTTCACCAACGTCAAGgtgcgacgcg ... cactccatagGAGGACATGATCATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTG
EST: gi|148942564|gb|EC887583.2|EC887583
EST:     CGGAAGGGAAAGGCTACTACATTGAGCCCACAGTTTTCACCAACGTCAAG                         GAGGACATGATCATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTG
genomic: CGGAAGGGAAAGGCTACTACATTGAGCCCACAGTTTTCACCAACGTCAAGgtgcgacgcg ... cactccatagGAGGACATGATCATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTG
EST: gi|76020436|gb|DT947606.1|DT947606
EST:     CGGAAGGGAAAGGCTACTACATTGAGCCCACAGTTTTCACCAACGTCAAG                         GAGGACATGATCATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTG
genomic: CGGAAGGGAAAGGCTACTACATTGAGCCCACAGTTTTCACCAACGTCAAGgtgcgacgcg ... cactccatagGAGGACATGATCATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTG
EST: gi|78083932|gb|DV512325.1|DV512325
EST:     CGGAAGGGAAAGGCTACTACATTGAGCCCACAGTTTTCACCAACGTCAAG                         GAGGACATGATCATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTG
genomic: CGGAAGGGAAAGGCTACTACATTGAGCCCACAGTTTTCACCAACGTCAAGgtgcgacgcg ... cactccatagGAGGACATGATCATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTG
EST: gi|149087182|gb|EE176719.2|EE176719
EST:     CGGAAGGGAAAGGCTACTACATTGAGCCCACAGTTTTCACCAACGTCAAG                         GAGGACATGATCATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTG
genomic: CGGAAGGGAAAGGCTACTACATTGAGCCCACAGTTTTCACCAACGTCAAGgtgcgacgcg ... cactccatagGAGGACATGATCATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTG
EST: gi|4835135|gb|AI670361.1|AI670361
EST:     CGGAAGGGAAAGGCTACTACATTGAGCCCACAGTTTTCACCAACGTCAAG                         GAGGACATGATCATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTG
genomic: CGGAAGGGAAAGGCTACTACATTGAGCCCACAGTTTTCACCAACGTCAAGgtgcgacgcg ... cactccatagGAGGACATGATCATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTG
EST: gi|78074898|gb|DV503332.1|DV503332
EST:     CGGAAGGGAAAGGCTACTACATTGAGCCCACAGTTTTCACCAACGTCAAG                         GAGGACATGATCATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTG
genomic: CGGAAGGGAAAGGCTACTACATTGAGCCCACAGTTTTCACCAACGTCAAGgtgcgacgcg ... cactccatagGAGGACATGATCATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTG
EST: gi|148959027|gb|EC905199.2|EC905199
EST:     CGGAAGGGAAAGGCTACTACATTGAGCCCACAGTTTTCACCAACGTCAAG                         GAGGACATGATCATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTG
genomic: CGGAAGGGAAAGGCTACTACATTGAGCCCACAGTTTTCACCAACGTCAAGgtgcgacgcg ... cactccatagGAGGACATGATCATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTG
EST: gi|211155790|gb|FL451802.1|FL451802
EST:     CGGAAGGGAAAGGCTACTACATTGAGCCCMCAGTTTTCACCAACGTCAAG                         GAGGACATGATCATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTG
genomic: CGGAAGGGAAAGGCTACTACATTGAGCCCACAGTTTTCACCAACGTCAAGgtgcgacgcg ... cactccatagGAGGACATGATCATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTG
EST: gi|148948769|gb|EC894170.2|EC894170
EST:     CGGAAGGGAAAGGCTACTACATTGAGCCCACAGTTTTCACCAACGTCAAG                         GAGGACATGATCATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTG
genomic: CGGAAGGGAAAGGCTACTACATTGAGCCCACAGTTTTCACCAACGTCAAGgtgcgacgcg ... cactccatagGAGGACATGATCATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTG
EST: gi|78091392|gb|DV519766.1|DV519766
EST:     CGGAAGGGAAAGGCTACTACATTGAGCCCACAGTTTTCACCAACGTCAAG                         GAGGACATGATCATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTG
genomic: CGGAAGGGAAAGGCTACTACATTGAGCCCACAGTTTTCACCAACGTCAAGgtgcgacgcg ... cactccatagGAGGACATGATCATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTG
EST: gi|71317747|gb|DR795632.1|DR795632
EST:     CGGAAGGGAAAGGCTACTACATTGAGCCCACAGTTTTCACCAACGTCAAG                         GAGGACATGATCATAGCGAAGGAGGAGATCCTCGGACCCGTCATGTGCCTG
genomic: CGGAAGGGAAAGGCTACTACATTGAGCCCACAGTTTTCACCAACGTCAAGgtgcgacgcg ... cactccatagGAGGACATGATCATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTG
EST: gi|148950305|gb|EC895864.2|EC895864
EST:     CGGAAGGGAAAGGCTACTACATTGAGCCCACAGTTTTCACCAACGTCAAG                         GAGGACATGATCATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTG
genomic: CGGAAGGGAAAGGCTACTACATTGAGCCCACAGTTTTCACCAACGTCAAGgtgcgacgcg ... cactccatagGAGGACATGATCATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTG
EST: gi|33468129|gb|CF245178.1|CF245178
EST:     CGGAAGGGAAAGGCTACTACATTGAGCCCACAGTTTTCACCAACGTCAAG                         GAGGACATGATCATAGCGAAGGAGGAGATCTTCGGACCTCGTCATGTGCCT
genomic: CGGAAGGGAAAGGCTACTACATTGAGCCCACAGTTTTCACCAACGTCAAGgtgcgacgcg ... cactccatagGAGGACATGATCATAGCGAAGGAGGAGATCTTCGGACC-CGTCATGTGCCT
EST: gi|148993480|gb|EE033799.2|EE033799
EST:     CGGAAGGGAAAGGCTACTACATTGAGCCCACAGTTTTCACCAACGTCAAG                         GAGGACATGATCATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTG
genomic: CGGAAGGGAAAGGCTACTACATTGAGCCCACAGTTTTCACCAACGTCAAGgtgcgacgcg ... cactccatagGAGGACATGATCATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTG
EST: gi|71426117|gb|DR807167.1|DR807167
EST:     CGGAAGGGAAAGGCTACTACATTGAGCCCACAGTTTTCACCAACGTCAAG                         GAGGACATGATCATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTG
genomic: CGGAAGGGAAAGGCTACTACATTGAGCCCACAGTTTTCACCAACGTCAAGgtgcgacgcg ... cactccatagGAGGACATGATCATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTG

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 3 RNA-Seq libraries.


Block sizes: 44 (upstream exon), 20 (downstream exon)
Score: 4

TGGCAAGCGAGAAGGGGCCACTCTTCTGACTGGAGGAAGGCCATGCGGTCCGGAAGGGAAAGGCTACTACATTGAGCCCACAGTTTTCACCAACGTCAAGgtgcgacgcg ... cactccatagGAGGACATGATCATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTGATGAAGTTCAA


Block sizes: 37 (upstream exon), 40 (downstream exon)
Score: 10

TGGCAAGCGAGAAGGGGCCACTCTTCTGACTGGAGGAAGGCCATGCGGTCCGGAAGGGAAAGGCTACTACATTGAGCCCACAGTTTTCACCAACGTCAAGgtgcgacgcg ... cactccatagGAGGACATGATCATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTGATGAAGTTCAA


Block sizes: 44 (upstream exon), 8 (downstream exon)
Score: 3

TGGCAAGCGAGAAGGGGCCACTCTTCTGACTGGAGGAAGGCCATGCGGTCCGGAAGGGAAAGGCTACTACATTGAGCCCACAGTTTTCACCAACGTCAAGgtgcgacgcg ... cactccatagGAGGACATGATCATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTGATGAAGTTCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagagatgacttttcttcttcttttttttctcccccttcttcttccactccatagGAGGACATGATCATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTGATGAAGTTCAA
         cttttcttcttctttt  CT-rich tract
               ttcttctttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgacgcgaacgaacactagtgcgacagttatatatacgtactactacgtacagtctagcttcaccgtctgacatgcatgagagatgacttttcttcttcttttttttctcccccttcttcttccactccatagGAGGACATGATCATAGCGAAGGAGGAGATCTTCGGACCCGTCATGTGCCTGATGAAGTTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC