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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACTCGTGTTCAGTTCCACCAAGATCAAATGCACTTTCTTGTTGTGCATGAAACCCAGATTGCCATCTATGAAACTACAAAACTAGAACCAGTGAAGCAGgtaaactgtctcctcacttgtctgcagattacacttgcaatggagttcagtatgttctcatttcccaccataacttcacttacag

Basic information

species Zea mays
transcript GRMZM2G550865_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G550865_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os03g14980.1 (Oryza sativa), 5'ss of exon 24
CACTCGTGTTCAGTTCCACCAAGATCAAATGCACTTTCTTGTTGTGCATGAAACCCAGATTGCCATCTATGAAACTACAAAACTAGAACCAGTGAAGCAGgtaaactgtctcctcacttgtctgcagattacacttgcaatggagttcagtatgttctcatttcccaccataacttcacttacag
||| |||||||||||||| || |||||| |||||||||||||||||||||| |||||||||||||| ||||||||||||||| ||||||| |||||||||||||| | |||| |||| ||    ||| | |   |  | |   ||   |      | ||||| | |||| |||||| |||| |||
CACACGTGTTCAGTTCCATCAGGATCAATTGCACTTTCTTGTTGTGCATGAGACCCAGATTGCCATATATGAAACTACAAAATTAGAACCCGTGAAGCAGgtaaattctctcttcacgtg----cagttcaagttaactacaaaggcta------tttcattactcaccttaactttactttcag
















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|211016175|gb|FL013379.1|FL013379
EST:     AAACCCAGATTGCCATCTATGAAACTACAAAACTAGAACCAGTGAAGCAG                         TGGCCTGTTCGAGAGAATTCACCTCCAATCACACATGCTGCATTCTCGTGT
genomic: AAACCCAGATTGCCATCTATGAAACTACAAAACTAGAACCAGTGAAGCAGgtaaactgtc ... tcacttacagTGGCCTGTTCGAGAGAATTCACCTCCAATCACACATGCTGCATTCTCGTGT
EST: gi|19057713|gb|BM736380.1|BM736380
EST:     AAACCCAGATTGCCATCTATGAAACTACAAAACTAGAACCAGTGAAGCAG                         TGGCCTGTTCGAGAGAATTCACCTCCAATCACACATGCTGCATTCTCGTGT
genomic: AAACCCAGATTGCCATCTATGAAACTACAAAACTAGAACCAGTGAAGCAGgtaaactgtc ... tcacttacagTGGCCTGTTCGAGAGAATTCACCTCCAATCACACATGCTGCATTCTCGTGT
EST: gi|19436915|gb|BM953325.1|BM953325
EST:     AAACCCAGATTGCCATCTATGAAACTACAAAACTAGAACCAGTGAAGCAG                         TGGCCTGTTCGAGAGAATTCACCTCCAATCACACATGCTGCATTCTCGTGT
genomic: AAACCCAGATTGCCATCTATGAAACTACAAAACTAGAACCAGTGAAGCAGgtaaactgtc ... tcacttacagTGGCCTGTTCGAGAGAATTCACCTCCAATCACACATGCTGCATTCTCGTGT
EST: gi|116814517|gb|EC857089.1|EC857089
EST:     AAACCCAGATTGCCATCTATGAAACTACAAAAC-AGAACCAGTGAAGCAG                         TGGCCTGTTCGAGAGAATTCACCTCCAATCACACATGCTGCATTCTCGTGT
genomic: AAACCCAGATTGCCATCTATGAAACTACAAAACTAGAACCAGTGAAGCAGgtaaactgtc ... tcacttacagTGGCCTGTTCGAGAGAATTCACCTCCAATCACACATGCTGCATTCTCGTGT
EST: gi|67024360|gb|CO453109.1|CO453109
EST:     AAACCCAGATTGCCATCTATGAAACTACAAAACTAGAACCAGTGAAGCAG                         TGGCCTGTTCGAGAGAATTCACCTCCAATCACACATGCTGCATTCTCGTGT
genomic: AAACCCAGATTGCCATCTATGAAACTACAAAACTAGAACCAGTGAAGCAGgtaaactgtc ... tcacttacagTGGCCTGTTCGAGAGAATTCACCTCCAATCACACATGCTGCATTCTCGTGT
EST: gi|19057573|gb|BM736240.1|BM736240
EST:     AAACCCAGATTGCCATCTATGAAACTACAAAACTAGAACCAGTGAAGCAG                         TGGCCCTGGTTCCGAGAGAATTCACCTCCAATCACACATGCTGCATTCTCG
genomic: AAACCCAGATTGCCATCTATGAAACTACAAAACTAGAACCAGTGAAGCAGgtaaactgtc ... tcacttacagTGG-CCT-GTT-CGAGAGAATTCACCTCCAATCACACATGCTGCATTCTCG
EST: gi|88747083|gb|DY531224.1|DY531224
EST:     AAACCCAGATTGCCATCTATGAAACTACAAAACTAGAACCAGTGAAGCAG                         TGGCCTGTGCGAGAGAATTCACCTCCAATCACACATGCTGCATTCTCGTGT
genomic: AAACCCAGATTGCCATCTATGAAACTACAAAACTAGAACCAGTGAAGCAGgtaaactgtc ... tcacttacagTGGCCTGTTCGAGAGAATTCACCTCCAATCACACATGCTGCATTCTCGTGT
EST: gi|19436916|gb|BM953326.1|BM953326
EST:     AAACCCAGATTGCCATCTATGAAACTACAAAACTAGAACCAGTGAAGCAG                         TGGCCTGTTCGAGAGAATTCACCTCCAATCACACATGCTGCATTCTCGTGT
genomic: AAACCCAGATTGCCATCTATGAAACTACAAAACTAGAACCAGTGAAGCAGgtaaactgtc ... tcacttacagTGGCCTGTTCGAGAGAATTCACCTCCAATCACACATGCTGCATTCTCGTGT
EST: gi|7216838|gb|AW562960.1|AW562960
EST:     AGATTGCCATCTATGAAACTACAAAACTAGAACCAGTGAAGCAG                         TGGCCTGTTCGAGAGAATTCACCTCCAATCACACATGCTGCATTCTCGTGT
genomic: AGATTGCCATCTATGAAACTACAAAACTAGAACCAGTGAAGCAGgtaaactgtc ... tcacttacagTGGCCTGTTCGAGAGAATTCACCTCCAATCACACATGCTGCATTCTCGTGT
EST: gi|67032677|gb|CO461426.1|CO461426
EST:     ANACCCAGATTGCCATCTATGAAACTACAAAACTAGAACCAGTGAAGCAG                         TGGCCTGTTCGAGAGAAT-CACCTCCAATCACACATGCTGCATTCTCGTGT
genomic: AAACCCAGATTGCCATCTATGAAACTACAAAACTAGAACCAGTGAAGCAGgtaaactgtc ... tcacttacagTGGCCTGTTCGAGAGAATTCACCTCCAATCACACATGCTGCATTCTCGTGT
EST: gi|87157645|gb|DY402434.1|DY402434
EST:     AAACCCAGATTGCCATCTATGAAACTACAAAACTAGAACCAGTGAAGCAG                         TGGCCTGTTCGAGAGA-TTCACCTCCAATCACACATGCTGCATTCTCGTGT
genomic: AAACCCAGATTGCCATCTATGAAACTACAAAACTAGAACCAGTGAAGCAGgtaaactgtc ... tcacttacagTGGCCTGTTCGAGAGAATTCACCTCCAATCACACATGCTGCATTCTCGTGT
EST: gi|19437048|gb|BM953458.1|BM953458
EST:     AAACCCAGA-TGCCATCTATGAAACTACAAAACTAGAACCAGTGAAGCAG                         TGGCCTGTTCGAGAGAATTCACCTCCAATCACACATGCTGCATTCTCGTGT
genomic: AAACCCAGATTGCCATCTATGAAACTACAAAACTAGAACCAGTGAAGCAGgtaaactgtc ... tcacttacagTGGCCTGTTCGAGAGAATTCACCTCCAATCACACATGCTGCATTCTCGTGT
EST: gi|31357352|gb|CD441709.1|CD441709
EST:     AAACCCAGATTGCCATCTATGAAACTACAAAACTAGAACCAGTGAAGCAG                         TGGCCTGTTCGAGAGAATTCACCTCCAATCACACATGCTGCATTCTCGTGT
genomic: AAACCCAGATTGCCATCTATGAAACTACAAAACTAGAACCAGTGAAGCAGgtaaactgtc ... tcacttacagTGGCCTGTTCGAGAGAATTCACCTCCAATCACACATGCTGCATTCTCGTGT
EST: gi|60345367|gb|DN212340.1|DN212340
EST:     AAACCCAGATTGCCATCTATGAAACTACAAAACTAGAACCAGTGAAGCAG                         TGGCCTGTTCGAGAGAATTCACCTCCAATCACACATGCTGCATTCTCGTGT
genomic: AAACCCAGATTGCCATCTATGAAACTACAAAACTAGAACCAGTGAAGCAGgtaaactgtc ... tcacttacagTGGCCTGTTCGAGAGAATTCACCTCCAATCACACATGCTGCATTCTCGTGT
EST: gi|78083755|gb|DV512148.1|DV512148
EST:     AAACCCAGATTGCCATCTATGAAACTACAAAACTAGAACCAGTGAAGCAG                         TGGCCTGTTCGAGAGAATTCACCTCCAATCACACATGCTGCATTCTCGTGT
genomic: AAACCCAGATTGCCATCTATGAAACTACAAAACTAGAACCAGTGAAGCAGgtaaactgtc ... tcacttacagTGGCCTGTTCGAGAGAATTCACCTCCAATCACACATGCTGCATTCTCGTGT

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: 837

CACTCGTGTTCAGTTCCACCAAGATCAAATGCACTTTCTTGTTGTGCATGAAACCCAGATTGCCATCTATGAAACTACAAAACTAGAACCAGTGAAGCAGgtaaactgtc ... tcacttacagTGGCCTGTTCGAGAGAATTCACCTCCAATCACACATGCTGCATTCTCGTGTGACAGTCAACTGATCTATGCAAGCTTTATGGATGCCACTGTTGGCATAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 546

CACTCGTGTTCAGTTCCACCAAGATCAAATGCACTTTCTTGTTGTGCATGAAACCCAGATTGCCATCTATGAAACTACAAAACTAGAACCAGTGAAGCAGgtaaactgtc ... tcacttacagTGGCCTGTTCGAGAGAATTCACCTCCAATCACACATGCTGCATTCTCGTGTGACAGTCAACTGATCTATGCAAGCTTTATGGATGCCACTGTTGGCATAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 750

CACTCGTGTTCAGTTCCACCAAGATCAAATGCACTTTCTTGTTGTGCATGAAACCCAGATTGCCATCTATGAAACTACAAAACTAGAACCAGTGAAGCAGgtaaactgtc ... tcacttacagTGGCCTGTTCGAGAGAATTCACCTCCAATCACACATGCTGCATTCTCGTGTGACAGTCAACTGATCTATGCAAGCTTTATGGATGCCACTGTTGGCATAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 661

CACTCGTGTTCAGTTCCACCAAGATCAAATGCACTTTCTTGTTGTGCATGAAACCCAGATTGCCATCTATGAAACTACAAAACTAGAACCAGTGAAGCAGgtaaactgtc ... tcacttacagTGGCCTGTTCGAGAGAATTCACCTCCAATCACACATGCTGCATTCTCGTGTGACAGTCAACTGATCTATGCAAGCTTTATGGATGCCACTGTTGGCATAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACTCGTGTTCAGTTCCACCAAGATCAAATGCACTTTCTTGTTGTGCATGAAACCCAGATTGCCATCTATGAAACTACAAAACTAGAACCAGTGAAGCAGgtaaactgtctcctcacttgtctgcagattacacttgcaatggagttcagtatgttctcatttcccaccataacttcacttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC