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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGGGCCGTAGACAAGAATTATCACTTGAAGATGAAAGCGTCAAGGTTTATTTTCAGTGAGATCAGCCAGAAGTTCCCAATCATGCCTTTTACTGCTAGgtttgtgactgcacaacgatttttgatttttgaagtgttctacttttgttgtgtactgaaacatgagcttatgaattgctatag

Basic information

species Zea mays
transcript AC233895.1_FGT001
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC233895.1_FGT001 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os05g28280.1 (Oryza sativa), 5'ss of exon 7
AAAGGGCCGTAGACAAGAATTATCACTTGAAGATGAAAGCGTCAAGGTTTATTTTCAGTGAGATCAGCCAGAAGTTCCCAATCATGCCTTTTACTGCTAGgtttgtgactgcacaacgatttttgatttttgaagtgttctacttttgttgtgtactgaaacatgagcttatgaattgctatag
| || || |||||||||||||||||||||||||||||||| || ||||| |||||||||||||| ||||||||||| || |||||||| || |||||||||||  |      ||||  |   || | ||  || |     |  | || |  | || || ||||||   || |||||||  | ||
AGAGAGCTGTAGACAAGAATTATCACTTGAAGATGAAAGCATCTAGGTTCATTTTCAGTGAGATAAGCCAGAAGTTTCCTATCATGCCCTTCACTGCTAGgttgct------acaataacgctt-acttcagacgcacctttttgtt-tactatattgtaacatgcattt-tgaattgtcacag

upper sequence: AC233895.1_FGT001 (Zea mays), 5'ss of exon 6
lower sequence: EFJ35350 (Selaginella moellendorffii), 5'ss of exon 6
AAAGGGCCGTAGACAAGAATTATCACTTGAAGATGAAAGCGTCAAGGTTTATTTTCAGTGAGATCAGCCAGAAGTTCCCAATCATGCCTTTTACTGCTAGgtttgtgactgcacaacgatttttgatttttgaagtgttctacttt-tgttgtgtactgaaacatgagcttatgaattgctatag
    |||||| |||||||  ||||| ||||||||||| || || |||||||| |||||||| || ||||||||||||||  ||||||| ||||| || |||   ||   |   |    ||| |    || ||  | | || | |||   || |  |  ||                         
----GGCCGTGGACAAGAGCTATCATTTGAAGATGAAGGCCTCGAGGTTTATATTCAGTGAAATAAGCCAGAAGTTCCCGCTCATGCCCTTTACCGCCAGGCAAgtt-ttcttctgtaattctatccttctggtgagctcaaatttgcattttccagggag------------------------

upper sequence: AC233895.1_FGT001 (Zea mays), 5'ss of exon 6
lower sequence: EFJ10608 (Selaginella moellendorffii), 5'ss of exon 6
AAAGGGCCGTAGACAAGAATTATCACTTGAAGATGAAAGCGTCAAGGTTTATTTTCAGTGAGATCAGCCAGAAGTTCCCAATCATGCCTTTTACTGCTAGgtttgtgactgcacaacgatttttgatttttgaagtgttct-acttttgttgtgtactgaaacatgagcttatgaattgctatag
    |||||| |||||||  ||||| ||||||||||| || || |||||||| |||||||| || ||||||||||| ||  ||||||| ||||| || |||   ||   |       |   ||  ||  ||   |||  || |  ||||   | | | |  |                       
----GGCCGTGGACAAGAGCTATCATTTGAAGATGAAGGCCTCGAGGTTTATATTCAGTGAAATAAGCCAGAAGTTTCCGCTCATGCCCTTTACCGCCAGGCAAgttgttttcttctgtaattctatccttccggtgagctcaaatttgcattttccagggag----------------------

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|32932980|gb|CF037792.1|CF037792
EST:     TTTTCAGTGAGATCAGCCAGAAGGTTCCCAATCATGCCTTTTACTGCTAG                         GGCATTAGAAGAGAAGCGTGCGCGTTTAGGCTTGGTGGAATGCATGAACCA
genomic: TTTTCAGTGAGATCAGCCAGAAG-TTCCCAATCATGCCTTTTACTGCTAGgtttgtgact ... attgctatagGGCATTAGAAGAGAAGCGTGCGCGTTTAGGCTTGGTGGAATGCATGAACCA
EST: gi|31351014|gb|CD435371.1|CD435371
EST:     ATTTTCAGTGAGATCAGCCAGAAGTTCCCAATCATGCCTTTTACTGCTAG                         GGCATTAGAAGAGAAGCGTGCGCGTTTAGGCTTGGTGGAATGCATGAACCA
genomic: ATTTTCAGTGAGATCAGCCAGAAGTTCCCAATCATGCCTTTTACTGCTAGgtttgtgact ... attgctatagGGCATTAGAAGAGAAGCGTGCGCGTTTAGGCTTGGTGGAATGCATGAACCA
EST: gi|14569289|gb|BI097612.1|BI097612
EST:     ATTTTCAGTGAGATCAGCCAGAAGTTCCCAATCATGCCTTTTACTGCTAG                         GGCATTAGAAGAGAAGCGTGCGCGTTTAGGCTTGGTGGAATGCATGAACCA
genomic: ATTTTCAGTGAGATCAGCCAGAAGTTCCCAATCATGCCTTTTACTGCTAGgtttgtgact ... attgctatagGGCATTAGAAGAGAAGCGTGCGCGTTTAGGCTTGGTGGAATGCATGAACCA
EST: gi|32850813|gb|CD990494.1|CD990494
EST:     ATTTTCAGTGAGATCAGCCAGAAGTTCCCAATCATGCCTTTTACTGCTAG                         GGCATTAGAAGAGAAGCGTGCGCGTTTAGGCTTGGTGGAATGCATGAACCA
genomic: ATTTTCAGTGAGATCAGCCAGAAGTTCCCAATCATGCCTTTTACTGCTAGgtttgtgact ... attgctatagGGCATTAGAAGAGAAGCGTGCGCGTTTAGGCTTGGTGGAATGCATGAACCA
EST: gi|84980121|gb|DW530470.1|DW530470
EST:     ATTTTCAGTGAGATCAGCCAGAAGTTCCCAATCATGCCTTTTACTGCTAG                         GGCATTAGAAGAGAAGCGTGCGCGTTTAGGCTTGGTGGAATGCATGAACCA
genomic: ATTTTCAGTGAGATCAGCCAGAAGTTCCCAATCATGCCTTTTACTGCTAGgtttgtgact ... attgctatagGGCATTAGAAGAGAAGCGTGCGCGTTTAGGCTTGGTGGAATGCATGAACCA
EST: gi|8665685|gb|BE186501.1|BE186501
EST:     ATTTTCAGTGAGATCAGCCAGAAGTTCCCAATCATGCCTTTTACTGCTAG                         GGCATTAGAAGAGAAGCGTGCGCGTTTAGGCTTGGTGGAATGCATGAACCA
genomic: ATTTTCAGTGAGATCAGCCAGAAGTTCCCAATCATGCCTTTTACTGCTAGgtttgtgact ... attgctatagGGCATTAGAAGAGAAGCGTGCGCGTTTAGGCTTGGTGGAATGCATGAACCA
EST: gi|32931969|gb|CF036781.1|CF036781
EST:     TTTTCAGTGAGATCAGCCAGAAGGTTCCCAATCATGCCTTTTACTGCTAG                         GGCATTAGAAGAGAAGCGTGCGCGTTTAGGCTTGGTGGAATGCATGAACCA
genomic: TTTTCAGTGAGATCAGCCAGAAG-TTCCCAATCATGCCTTTTACTGCTAGgtttgtgact ... attgctatagGGCATTAGAAGAGAAGCGTGCGCGTTTAGGCTTGGTGGAATGCATGAACCA
EST: gi|33097827|gb|CF057787.1|CF057787
EST:     ATTTTCAGTGAGATCAGCCAGAAGTTCCCAATCATGCCTTTTACTGCTAG                         GGCATTAGAAGAGAAGCGTGCGCGTTTAGGCTTGGTGGAATGCATGAACCA
genomic: ATTTTCAGTGAGATCAGCCAGAAGTTCCCAATCATGCCTTTTACTGCTAGgtttgtgact ... attgctatagGGCATTAGAAGAGAAGCGTGCGCGTTTAGGCTTGGTGGAATGCATGAACCA
EST: gi|32838111|gb|CD977789.1|CD977789
EST:     TTTTCAGTGAGATCAGCCAGAAGTTAAACAATCATGCCTTTTACTGCTAG                         GGCATTAGAAGAGAAGCGTGCGCGTTTAGGCTTGGTGGAATGCATGAACCA
genomic: TTTTCAGTGAGATCAGCCAGAAGTTCC-CAATCATGCCTTTTACTGCTAGgtttgtgact ... attgctatagGGCATTAGAAGAGAAGCGTGCGCGTTTAGGCTTGGTGGAATGCATGAACCA
EST: gi|32838243|gb|CD977921.1|CD977921
EST:     ATTTTCAGTGAGATCAGCCAGAAGTTAACAATCATGCCTTTTACTGCTAG                         GGCATTAGAAGAGAAGCGTGCGCGTTTAGGCTTGGTGGAATGCATGAACCA
genomic: ATTTTCAGTGAGATCAGCCAGAAGTTCCCAATCATGCCTTTTACTGCTAGgtttgtgact ... attgctatagGGCATTAGAAGAGAAGCGTGCGCGTTTAGGCTTGGTGGAATGCATGAACCA
EST: gi|32850802|gb|CD990483.1|CD990483
EST:     ATTTTCAGTGAGATCAGCCAGAAGTTCCCAATCATGCCTTTTACTGCTAG                         GGCATTAGAAGAGAAGCGTGCGCGTTTAGGCTTGGTGGAATGCATGAACCA
genomic: ATTTTCAGTGAGATCAGCCAGAAGTTCCCAATCATGCCTTTTACTGCTAGgtttgtgact ... attgctatagGGCATTAGAAGAGAAGCGTGCGCGTTTAGGCTTGGTGGAATGCATGAACCA
EST: gi|166427588|gb|EG314516.1|EG314516
EST:     ATTTTCAGTGAGATCAGCCAGAAGTTCCCAATCATGCCTTTTACTGCTAG                         GGCATTAGAAGAGAAGCGTGCGCGTTTAGGCTTGGTGGAA
genomic: ATTTTCAGTGAGATCAGCCAGAAGTTCCCAATCATGCCTTTTACTGCTAGgtttgtgact ... attgctatagGGCATTAGAAGAGAAGCGTGCGCGTTTAGGCTTGGTGGAA
EST: gi|33092800|gb|CF052794.1|CF052794
EST:     TTTTCAGTGAGATCAGCCAGAAGGTTCCCAAACATGCCTTTTACTACTAG                         GGCATTAGAAGAGAAGCGTGCGCGTTTAGGCTTGGTGGAATGCATGAACCA
genomic: TTTTCAGTGAGATCAGCCAGAAG-TTCCCAATCATGCCTTTTACTGCTAGgtttgtgact ... attgctatagGGCATTAGAAGAGAAGCGTGCGCGTTTAGGCTTGGTGGAATGCATGAACCA
EST: gi|15208836|gb|BI430720.1|BI430720
EST:     ATTTTCAGTGAGATCAGCCAGAAGTTCCCAATCATGCCTTTTACTGCTAG                         GGCATTAGAAGAGAAGCGTGCGCGTTTAGGCTTGGTGGAATGCATGAACCA
genomic: ATTTTCAGTGAGATCAGCCAGAAGTTCCCAATCATGCCTTTTACTGCTAGgtttgtgact ... attgctatagGGCATTAGAAGAGAAGCGTGCGCGTTTAGGCTTGGTGGAATGCATGAACCA

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: 49 (upstream exon), 49 (downstream exon)
Score: 581

AAAGGGCCGTAGACAAGAATTATCACTTGAAGATGAAAGCGTCAAGGTTTATTTTCAGTGAGATCAGCCAGAAGTTCCCAATCATGCCTTTTACTGCTAGgtttgtgact ... attgctatagGGCATTAGAAGAGAAGCGTGCGCGTTTAGGCTTGGTGGAATGCATGAACCATGAACTATTGCAGCCGTACCCTGTACTTCATGAGAAGCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 384

AAAGGGCCGTAGACAAGAATTATCACTTGAAGATGAAAGCGTCAAGGTTTATTTTCAGTGAGATCAGCCAGAAGTTCCCAATCATGCCTTTTACTGCTAGgtttgtgact ... attgctatagGGCATTAGAAGAGAAGCGTGCGCGTTTAGGCTTGGTGGAATGCATGAACCATGAACTATTGCAGCCGTACCCTGTACTTCATGAGAAGCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 504

AAAGGGCCGTAGACAAGAATTATCACTTGAAGATGAAAGCGTCAAGGTTTATTTTCAGTGAGATCAGCCAGAAGTTCCCAATCATGCCTTTTACTGCTAGgtttgtgact ... attgctatagGGCATTAGAAGAGAAGCGTGCGCGTTTAGGCTTGGTGGAATGCATGAACCATGAACTATTGCAGCCGTACCCTGTACTTCATGAGAAGCCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 365

AAAGGGCCGTAGACAAGAATTATCACTTGAAGATGAAAGCGTCAAGGTTTATTTTCAGTGAGATCAGCCAGAAGTTCCCAATCATGCCTTTTACTGCTAGgtttgtgact ... attgctatagGGCATTAGAAGAGAAGCGTGCGCGTTTAGGCTTGGTGGAATGCATGAACCATGAACTATTGCAGCCGTACCCTGTACTTCATGAGAAGCCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAGGGCCGTAGACAAGAATTATCACTTGAAGATGAAAGCGTCAAGGTTTATTTTCAGTGAGATCAGCCAGAAGTTCCCAATCATGCCTTTTACTGCTAGgtttgtgactgcacaacgatttttgatttttgaagtgttctacttttgttgtgtactgaaacatgagcttatgaattgctatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT