Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTGACGGATACCCAACAATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCTgtaagtgcttatcattttacctgttgatgtgtggtatcctgtaatcacattattctcagcagtgctatctttatgaacattgactgattcgatgtgttggtag

Basic information

species Zea mays
transcript GRMZM2G033829_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G033829_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os02g01010.1 (Oryza sativa), 5'ss of exon 11
TCTGACGGATACCCAACAATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCTgtaagtgcttatcattttacctgttgatgtgtggtatcctgtaatcacattattctcagcagtgctatctttatgaacattgactgattcgatgtgttggtag---
 |||| |||| |||||| || ||||| |||||||| || |||||||| |||||||||||||||||  |  | | |   |  ||   | | |     || | |    ||| | |  | | | || ||| |  | |  ||   |   ||  | | | |||||   
CCTGATGGATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTTGAGCCTgtaagtgccca--aatatgtgtcatgtcttattgaggggtgcatttg--ttactgtatgtaat-ctgtctctcagtaggtttgttacctctctct-tcggtagaat

upper sequence: GRMZM2G033829_T01 (Zea mays), 5'ss of exon 10
lower sequence: PP1S122_5V6.1 (Physcomitrella patens), 5'ss of exon 12
TCTGACGGATACCCAACAATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCTgtaagtgcttatcattttacctgttgatgtgtggtatcctgtaatcac------attattctcagcagtgctatctttatgaa-----cattgactgat-tcgatgtgttggtag---------------------------------------------------------------
 | || || || || || ||||| |||| ||||||||||||||| ||||||||||| ||  ||  || |    ||  ||  ||| | | || ||    |  |||       |   | |     | ||  |   ||  |||     || ||| || | |  | |   || ||                                                                
CCCGATGGCTATCCGACTATTCTTTTCTTTCCAGCTGGGAAGAAGAGCTTTGAGCCAgtgcgtctttctatccttttctcctga-gcgaggaatttattgctcagtgctgaaccttgcatgagattggaacagttcagaatcatgcagtgaatgttcttcaggacctgataaccttgaagctatgtttgtaaattagaacttcattacttagagttgcaatgcttgacaatgcag
















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|211287726|gb|FL479937.1|FL479937
EST:     GATACCCAACAATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCT                         GTCACGTTTGAGGGGGAGCGGACAGTGGTAGATATGTACAGGTTCATCAAG
genomic: GATACCCAACAATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCTgtaagtgctt ... gtgttggtagGTCACGTTTGAGGGGGAGCGGACAGTGGTAGATATGTACAGGTTCATCAAG
EST: gi|88753885|gb|DY538026.1|DY538026
EST:     GATACCCAACAATTCTCTTTTATCCAGCTGGGAAGAAAAGCTTTGAGCCT                         GTCACGTTTGAGGGGGAGCGGACAGTGGTAGATATGTACAGGTTCATCAAG
genomic: GATACCCAACAATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCTgtaagtgctt ... gtgttggtagGTCACGTTTGAGGGGGAGCGGACAGTGGTAGATATGTACAGGTTCATCAAG
EST: gi|76293094|gb|DV032662.1|DV032662
EST:     GATACCCAACAATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCT                         GTCACGTTTGAGGGGGAGCGGACAGTGGTAGATATGTACAGGTTCATCAAG
genomic: GATACCCAACAATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCTgtaagtgctt ... gtgttggtagGTCACGTTTGAGGGGGAGCGGACAGTGGTAGATATGTACAGGTTCATCAAG
EST: gi|211432368|gb|FL434135.1|FL434135
EST:     GATACCCAACAATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCT                         GTCACGTTTGAGGGGGAGCGGACAGTGGTAGATATGTACAGGTTCATCAAG
genomic: GATACCCAACAATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCTgtaagtgctt ... gtgttggtagGTCACGTTTGAGGGGGAGCGGACAGTGGTAGATATGTACAGGTTCATCAAG
EST: gi|71331475|gb|DR802579.1|DR802579
EST:     GATACCCAACAATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCT                         GTCACGTTTGAGGGGGAGCGGACAGTGGTAGATATGTACAGGTTCATCAAG
genomic: GATACCCAACAATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCTgtaagtgctt ... gtgttggtagGTCACGTTTGAGGGGGAGCGGACAGTGGTAGATATGTACAGGTTCATCAAG
EST: gi|5770161|gb|AI973335.1|AI973335
EST:     GATACCCAACAATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCT                         GTCACTTTTGAGGGGGAGCGGACAGTGGTAGATATGTACAGGTTCATCAAG
genomic: GATACCCAACAATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCTgtaagtgctt ... gtgttggtagGTCACGTTTGAGGGGGAGCGGACAGTGGTAGATATGTACAGGTTCATCAAG
EST: gi|78113406|gb|DV531798.1|DV531798
EST:     GATACCCAACAATTCTTTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCT                         GTCACGTTTGAGGGGGAGCGGACAGTGGTAGATATGTACAGGTTCATCAAG
genomic: GATACCCAACAATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCTgtaagtgctt ... gtgttggtagGTCACGTTTGAGGGGGAGCGGACAGTGGTAGATATGTACAGGTTCATCAAG
EST: gi|5325044|gb|AI783235.1|AI783235
EST:     GATACCCAACAATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCT                         GTCACTTTTGAGGGGGAGCGGACAGTGGTAGATATGTACAGGTTCATCAAG
genomic: GATACCCAACAATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCTgtaagtgctt ... gtgttggtagGTCACGTTTGAGGGGGAGCGGACAGTGGTAGATATGTACAGGTTCATCAAG
EST: gi|211432367|gb|FL434134.1|FL434134
EST:     GATACCCAACAATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCT                         GTCACGTTTGAGGGGGAGCGGACAGTGGTAGATATGTACAGGTTCATCAAG
genomic: GATACCCAACAATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCTgtaagtgctt ... gtgttggtagGTCACGTTTGAGGGGGAGCGGACAGTGGTAGATATGTACAGGTTCATCAAG
EST: gi|5846856|gb|AI999939.1|AI999939
EST:     GATACCCAACAATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCT                         GTCACTTTTGAGGGGGAGCGGACAGNGGTAGATATGTACAGGTTCATCAAG
genomic: GATACCCAACAATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCTgtaagtgctt ... gtgttggtagGTCACGTTTGAGGGGGAGCGGACAGTGGTAGATATGTACAGGTTCATCAAG
EST: gi|110481095|gb|EE010948.1|EE010948
EST:     GATACCCAACAANNNNNNNCTATCCAGCTGGGAAGAAAAGCTTTGAGCCT                         GTCACGTTTGAGGGGGAGCGGACAGTGGTAGATATGTACAGGTTCATCAAG
genomic: GATACCCAACAATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCTgtaagtgctt ... gtgttggtagGTCACGTTTGAGGGGGAGCGGACAGTGGTAGATATGTACAGGTTCATCAAG

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: 73

TCTGACGGATACCCAACAATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCTgtaagtgctt ... gtgttggtagGTCACGTTTGAGGGGGAGCGGACAGTGGTAGATATGTACAGGTTCATCAAGAAACATGCTAGCATCCCTTTCAAGTTGAAGCGCCAGGAGTCAAGAAGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 84

TCTGACGGATACCCAACAATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCTgtaagtgctt ... gtgttggtagGTCACGTTTGAGGGGGAGCGGACAGTGGTAGATATGTACAGGTTCATCAAGAAACATGCTAGCATCCCTTTCAAGTTGAAGCGCCAGGAGTCAAGAAGGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 109

TCTGACGGATACCCAACAATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCTgtaagtgctt ... gtgttggtagGTCACGTTTGAGGGGGAGCGGACAGTGGTAGATATGTACAGGTTCATCAAGAAACATGCTAGCATCCCTTTCAAGTTGAAGCGCCAGGAGTCAAGAAGGG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 100

TCTGACGGATACCCAACAATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCTgtaagtgctt ... gtgttggtagGTCACGTTTGAGGGGGAGCGGACAGTGGTAGATATGTACAGGTTCATCAAGAAACATGCTAGCATCCCTTTCAAGTTGAAGCGCCAGGAGTCAAGAAGGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTGACGGATACCCAACAATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCTgtaagtgcttatcattttacctgttgatgtgtggtatcctgtaatcacattattctcagcagtgctatctttatgaacattgactgattcgatgtgttggtag

- - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - -  AAGAAA