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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATCAGGGAAAATGATATATTATACTTCATAATGGAATACATGgtaaatatgttatgtatagcaaatattctactgcaccattattgtgttcttgaatctgaacccttgtttttatag

Basic information

species Zea mays
transcript GRMZM2G178822_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G178822_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os02g47220.3 (Oryza sativa), 5'ss of exon 2
TCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATCAGGGAAAATGATATATTATACTTCATAATGGAATACATGgta----aatatgttatgtatagcaaatattctactgcaccattattg-tgttcttgaatctgaacccttgtttttatag
|||||||||||||||||||| |||||||| ||||||||||| |||||||| ||||||||||| ||||||||||||||||||||||||||||||    |  |||| || ||  |||||  ||  | |    |  ||| | | || || | |||   ||| |||| ||  ||
TCTTTGCGGCGCATGAATCACCCTAACATCGTGAAGCTCAAGGAGGTTATAAGGGAAAATGACATATTATACTTCATAATGGAATACATGgtacttaaggatgtcatataccgcaaaagtttaattagctctgtatcgcttttgttaagtct---cccatgttcttccag

upper sequence: GRMZM2G178822_T01 (Zea mays), 5'ss of exon 8
lower sequence: AT4G19110.1 (Arabidopsis thaliana), 5'ss of exon 6
TCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATCAGGGAAAATGATATATTATACTTCATAATGGAATACATGgtaaatatgttatgta-----tagcaaatattctactgcaccattattgtgttct-tgaatctgaacccttgtttttatag---------
||  |  || | ||||||||||| |||||||||||| | || || || ||| |||||||||||||  |||||||  |  | || ||||||||| |  | ||   |      |   |  |||| |     ||  |||||   | || ||||||| |     |||  || |           
TCGCTCAGGAGAATGAATCATCCAAACATTGTGAAGTTGAAGGAAGTAATCCGGGAAAATGATATCCTATACTTTGTCTTTGAGTACATGgtatacttctttcctgcttgttgttaggtattttctgatacttttattcattgctctgaatct-actttatgtcattctttcttgatcag

upper sequence: GRMZM2G178822_T01 (Zea mays), 5'ss of exon 8
lower sequence: AT5G45430.1 (Arabidopsis thaliana), 5'ss of exon 6
TCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATCAGGGAAAATGATATATTATACTTCATAATGGAATACATGgtaaatatgtt---atgtatagcaaatattctactgc-accattattgtgttcttgaatctgaacccttgtttttatag--------
||  |  |  | ||||||||||| |||||||||||||| || || || ||| |||||||||||||  |||||||  |  | || ||||||||| |  | ||   |  | | ||  | ||  || ||| | || | || | |   | |||||    | |   ||| |||         
TCACTTAGCAGAATGAATCATCCAAACATTGTGAAGCTGAAGGAAGTCATCCGGGAAAATGATATCCTATACTTTGTGTTTGAGTACATGgtatacttctttctactttttgctta-atcttattgccaacacttttttttctctaaatct---tcttccctttcatactctgtcag

upper sequence: GRMZM2G178822_T01 (Zea mays), 5'ss of exon 8
lower sequence: PP1S173_136V6.1 (Physcomitrella patens), 5'ss of exon 4
TCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATCAGGGAAAATGATATATTATACTTCATAATGGAATACATGgtaaa----tatgttat----------------gtatagcaaatattctactgcaccattattgtgttcttgaatctgaacccttgtttttatag---------------------------------
|||||||||    |||||||||||||||| |||||||| || ||||||||| | ||||| |||  | | |  ||| |  | || || ||||| |     ||  || |                ||| ||||| ||||  |  |     || || ||   || |||      | ||| | | |||                                  
TCTTTGCGGAAGCTGAATCATCCTAACATCGTGAAGCTGAAGGAGGTTATCCGTGAAAACGATGAACTGTTTTTCGTTTTTGAGTATATGgtgaggttttagcttttcacggctctagaaatggtacagcaattatttgatggtttgtttcttctgggattaaatgatggacattggtgtaatattcctttcaatattgtttgcatttaatcgtgcag

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|211443458|gb|FL042456.1|FL042456
EST:     AAGAGGTTATCAGGGAAAATGATATATTATACTTCATAATGGAATACATG                         GAGTGTAATCTCTATCAACTTATGAA
genomic: AAGAGGTTATCAGGGAAAATGATATATTATACTTCATAATGGAATACATGgtaaatatgt ... gtttttatagGAGTGTAATCTCTATCAACTTATGAA
EST: gi|211443465|gb|FL042463.1|FL042463
EST:     AAGAGGTTATCAGGGAAAATGATATATTATACTTCATAATGGAATACATG                         GAGTGTAATCTCTATCAACTTATGAAAGAAAGGGTCA
genomic: AAGAGGTTATCAGGGAAAATGATATATTATACTTCATAATGGAATACATGgtaaatatgt ... gtttttatagGAGTGTAATCTCTATCAACTTATGAAAGAAAGGGTCA
EST: gi|60345317|gb|DN212290.1|DN212290
EST:     AAGAGGTTATCAGGGAAAATGATATATTATACTTCATAATGGAATACATG                         GAGTGTAATCTCTATCAACTTATGAAAGAAAGGGTCAAGCCTTTCTCCGAG
genomic: AAGAGGTTATCAGGGAAAATGATATATTATACTTCATAATGGAATACATGgtaaatatgt ... gtttttatagGAGTGTAATCTCTATCAACTTATGAAAGAAAGGGTCAAGCCTTTCTCCGAG
EST: gi|211443464|gb|FL042462.1|FL042462
EST:     AGAGGTTATCAGGGAAAATGATATATTATACTTCATAATGGAATACCATG                         GAGTGTAATCTCTATCAACTTATGAAAGA
genomic: AGAGGTTATCAGGGAAAATGATATATTATACTTCATAATGGAATAC-ATGgtaaatatgt ... gtttttatagGAGTGTAATCTCTATCAACTTATGAAAGA

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: 47 (upstream exon), 49 (downstream exon)
Score: 166

TCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATCAGGGAAAATGATATATTATACTTCATAATGGAATACATGgtaaatatgt ... gtttttatagGAGTGTAATCTCTATCAACTTATGAAAGAAAGGGTCAAGCCTTTCTCCGAGTCTGAAGTCCGCAACTGGTGTTTTCAGATATTTCAGGCTCTTGCATACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 125

TCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATCAGGGAAAATGATATATTATACTTCATAATGGAATACATGgtaaatatgt ... gtttttatagGAGTGTAATCTCTATCAACTTATGAAAGAAAGGGTCAAGCCTTTCTCCGAGTCTGAAGTCCGCAACTGGTGTTTTCAGATATTTCAGGCTCTTGCATACA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 77

TCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATCAGGGAAAATGATATATTATACTTCATAATGGAATACATGgtaaatatgt ... gtttttatagGAGTGTAATCTCTATCAACTTATGAAAGAAAGGGTCAAGCCTTTCTCCGAGTCTGAAGTCCGCAACTGGTGTTTTCAGATATTTCAGGCTCTTGCATACA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 158

TCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATCAGGGAAAATGATATATTATACTTCATAATGGAATACATGgtaaatatgt ... gtttttatagGAGTGTAATCTCTATCAACTTATGAAAGAAAGGGTCAAGCCTTTCTCCGAGTCTGAAGTCCGCAACTGGTGTTTTCAGATATTTCAGGCTCTTGCATACA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATCAGGGAAAATGATATATTATACTTCATAATGGAATACATGgtaaatatgttatgtatagcaaatattctactgcaccattattgtgttcttgaatctgaacccttgtttttatag

- - - - - - - - - - - - - - - - - - - - AAGAGG