Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTGAGATAAATTCTGGTGAGGGAGTTTACAAGGATAGCACACTTATGATGCAGCTTCTGAAGGACAACTTAGCATTGTGGACATCAGAACTAACTGGGGgtaatccatgtttgaaaaaaaatatacctttattatttgctatatagtggcctgcagagtactgacaatgctttacttgacattcctttgagccaaagct...

Basic information

species Zea mays
transcript GRMZM2G145213_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G145213_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os11g39540.1 (Oryza sativa), 5'ss of exon 5
ACTGAGATAAATTCT---GGTGAGGGAGTTTACAAGGATAGCACACTTATGATGCAGCTTCTGAAGGACAACTTAGCATTGTGGACATCAGAACTAACTGGGGgtaatccatgtttgaaaaaaaatat-----acctttattatttgctatatagtggcctgcagagtactgacaatgctttacttgacattcctttgagccaaagct
   ||||| || |||   |||| ||  | ||||||||| ||||  |||||||||||||| |||||||| ||| | |||||||||||||||||||||||||| |||||   |  |   | |||||||||     ||  | |   | || |  ||    || |   || ||  || |||  | |   | | ||    |  |   |     
---GAGATTAACTCTGCTGGTGTGGAGGGTTACAAGGACAGCATGCTTATGATGCAGCTCCTGAAGGAGAACCTGGCATTGTGGACATCAGAACTAACTGGAGgtaaatgaactacaataaaaaatattttcaacaatcaacttctgttgcatttctgctttttga-taaagagaatattctgtgttatatcttctatatatat----
















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|74234408|gb|DT642322.1|DT642322
EST:     CAGCTTTCTGA-GGACAACTTAGCATTGTGGACATCAGAACTAACTGGGG                         GTGAAGCATCCAAGGGTAACGGCGATGTCGACATGGAG
genomic: CAGCTT-CTGAAGGACAACTTAGCATTGTGGACATCAGAACTAACTGGGGgtaatccatg ... attttggcagGTGAAGCATCCAAGGGTAACGGCGATGTCGACATGGAG
EST: gi|211267022|gb|FK966686.1|FK966686
EST:     GCAGCTTCTGAAGGACAACTTAGCATTGTGGACATCAGAACTAACTGGAG                         GTGAAGCATCCAA
genomic: GCAGCTTCTGAAGGACAACTTAGCATTGTGGACATCAGAACTAACTGGGGgtaatccatg ... attttggcagGTGAAGCATCCAA
EST: gi|78093195|gb|DV521569.1|DV521569
EST:     GCAGCTTCTGAAGGACAACTTAGCATTGTGGACATCAGAACTAACTGGGG                         GTGAAGCATCCAAGGGTAACGGCGATGTCGACA
genomic: GCAGCTTCTGAAGGACAACTTAGCATTGTGGACATCAGAACTAACTGGGGgtaatccatg ... attttggcagGTGAAGCATCCAAGGGTAACGGCGATGTCGACA
EST: gi|101382257|gb|EB813184.1|EB813184
EST:     GCAGCTTCTGAAGGACAACTTAGCATTGTGGACATCAGAACTAACTGGGG                         GTGAAGCATCCAAGGGAAACGGCGATGT
genomic: GCAGCTTCTGAAGGACAACTTAGCATTGTGGACATCAGAACTAACTGGGGgtaatccatg ... attttggcagGTGAAGCATCCAAGGGTAACGGCGATGT
EST: gi|44681886|gb|CK786934.1|CK786934
EST:     GCAGCTTCTGAAGGACACCTTAGCATTGTGGACATCAGAACTAACTGGAG                         GTGAAGCATCCA
genomic: GCAGCTTCTGAAGGACAACTTAGCATTGTGGACATCAGAACTAACTGGGGgtaatccatg ... attttggcagGTGAAGCATCCA
EST: gi|71444597|gb|DR825647.1|DR825647
EST:     GCAGCTTCTGAAGGACAACTTAGCATTGTGGACATCAGAACTAACTGGGG                         GTGAAGCATCCAAGGGTAACGGCGATGTCGACATGGAG
genomic: GCAGCTTCTGAAGGACAACTTAGCATTGTGGACATCAGAACTAACTGGGGgtaatccatg ... attttggcagGTGAAGCATCCAAGGGTAACGGCGATGTCGACATGGAG

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: 367

ACTGAGATAAATTCTGGTGAGGGAGTTTACAAGGATAGCACACTTATGATGCAGCTTCTGAAGGACAACTTAGCATTGTGGACATCAGAACTAACTGGGGgtaatccatg ... attttggcagGTGAAGCATCCAAGGGTAACGGCGATGTCGACATGGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 182

ACTGAGATAAATTCTGGTGAGGGAGTTTACAAGGATAGCACACTTATGATGCAGCTTCTGAAGGACAACTTAGCATTGTGGACATCAGAACTAACTGGGGgtaatccatg ... attttggcagGTGAAGCATCCAAGGGTAACGGCGATGTCGACATGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 240

ACTGAGATAAATTCTGGTGAGGGAGTTTACAAGGATAGCACACTTATGATGCAGCTTCTGAAGGACAACTTAGCATTGTGGACATCAGAACTAACTGGGGgtaatccatg ... attttggcagGTGAAGCATCCAAGGGTAACGGCGATGTCGACATGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 198

ACTGAGATAAATTCTGGTGAGGGAGTTTACAAGGATAGCACACTTATGATGCAGCTTCTGAAGGACAACTTAGCATTGTGGACATCAGAACTAACTGGGGgtaatccatg ... attttggcagGTGAAGCATCCAAGGGTAACGGCGATGTCGACATGGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTGAGATAAATTCTGGTGAGGGAGTTTACAAGGATAGCACACTTATGATGCAGCTTCTGAAGGACAACTTAGCATTGTGGACATCAGAACTAACTGGGGgtaatccatgtttgaaaaaaaatatacctttattatttgctatatagtggcctgcagagtactgacaatgctttacttgacattcctttgagccaaagct

- - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaaa