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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATACAAGGTCCACTCCCACAATAGAAATGGGCTTTGTGCGGTTGCATTCATGGATGATCATTATCCGGTACGGAGTGCATTTTCTCTTCTGAATCAGgtaccaatcgttatcccctagactcccacttgccttttgcttttggtttaagcccaggttaccaattgtaagctgtagccagtcacttttcattctgttc...

Basic information

species Zea mays
transcript GRMZM2G387076_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G387076_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g64650.1 (Oryza sativa), 5'ss of exon 2
AATACAAGGTCCACTCCCACAATAGAAATGGGCTTTGTGCGGTTGCATTCATGGATGATCATTATCCGGTACGGAGTGCATTTTCTCTTCTGAATCAGgtaccaatcgttatcccctagactcccacttgccttttgcttttggtttaagcccaggttaccaattgtaagctgtagccagtcacttttcattctgttc---
|||||||||||||||| ||||| || ||||| ||||| || |||||||| ||||||||||| ||||| ||||| ||||||||||||||||||||| |||||  |  | || | |   | | |||    |  | | | ||| |  || |  || ||| |   | |   ||||  ||     |   | | | | || |||   
AATACAAGGTCCACTCACACAACAGGAATGGTCTTTGCGCAGTTGCATTTATGGATGATCACTATCCTGTACGAAGTGCATTTTCTCTTCTGAATAAGgtatgagcctttgttcttgacattcctgtattgcatatccttgtatttga--cctaggatcagattcacaagcaataagggattg-tctccttgctattctca

upper sequence: GRMZM2G387076_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA13G19950.1 (Glycine max), 5'ss of exon 2
AATACAAGGTCCACTCCCACAATAGAAATGGGCTTTGTGCGGTTGCATTCATGGATGATCATTATCCGGTACGGAGTGCATTTTCTCTTCTGAATCAGgtaccaatc-gttatcccctagactcccacttgccttttgcttttggtttaagcc-caggttaccaattgtaagctgtagccagtcact-tttcattctgttc--
| |||||||| ||| |  |||| |||||||| ||||| ||| | | ||| |||||||||||||| ||| | |||||||| ||||||||||| || |||||   | || | |  |   | || |    ||   |||  |  ||      | |      ||| |   ||| ||  | |||  ||  | | ||| |   ||     
AGTACAAGGTGCACACATACAACAGAAATGGTCTTTGCGCGTTGGGATTTATGGATGATCATTACCCGATTCGGAGTGCGTTTTCTCTTCTCAACCAGgtgagactcagatcactgttggatttttgctg--cttccgtattcaagacatgttattcgttgct--ttggaaaat-taggaagatattgtttgaaggtgcatga

upper sequence: GRMZM2G387076_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA09G13840.1 (Glycine max), 5'ss of exon 2
AATACAAGGTCCACTCCCACAATAGAAATGGGCTTTGTGCGGTTGCATTCATGGATGATCATTATCCGGTACGGAGTGCATTTTCTCTTCTGAATCAGgtaccaatcg--ttatccccta--gactcccacttgccttttgcttttggtttaagcccaggttaccaattgtaagctgtagccagtcacttttcattctgttc
| |||||||| ||| |  |||| || ||||| ||||| ||| | | ||| |||||||||||||| ||| | |||||||| ||||||||||| ||||||||   | ||   | | |   ||  |  ||     |   || |   ||||  || |    |  ||     ||      |||    |   |  |||  |  |    
AGTACAAGGTGCACACATACAACAGGAATGGTCTTTGCGCGTTGGGATTTATGGATGATCATTACCCGATTCGGAGTGCGTTTTCTCTTCTCAATCAGgtgagactcagataaccgtttattggttcagtgctatattgtatatttgtattcatggaattttgttgcttcctttgtgtctataaggaacttttttcat----

upper sequence: GRMZM2G387076_T02 (Zea mays), 5'ss of exon 3
lower sequence: AT5G58060.1 (Arabidopsis thaliana), 5'ss of exon 2
AATACAAGGTCCACTCCCACAATAGAAATGGGCTTTGTGCGGTTGCATTCATGGATGATCATTATCCGGTACGGAGTGCATTTTCTCTTCTGAATCAGgtaccaatcgttatcccctagactcccacttgccttttgcttttggtttaagcccaggttaccaattgtaagctgtagccagtcacttttcattctgttc---
| |||||||| ||| |  ||||||||||||| ||||| ||||| |  |||||||| |||||||| || || || ||||| || |||||||| |||||||||  | || ||||     |          ||  | |   |   |  | |  |  | |||  |   |||||  ||       | || ||| ||| |||     
AGTACAAGGTTCACGCTTACAATAGAAATGGCCTTTGCGCGGTGGGTTTCATGGACGATCATTACCCTGTTCGAAGTGCTTTCTCTCTTCTCAATCAGgtaata-tcattatgttgaaag--------tggttctcaat---gcatcattcgtaagttttc--ctgtaatttgggttgcttgacatttaattttgtctcag

upper sequence: GRMZM2G387076_T02 (Zea mays), 5'ss of exon 3
lower sequence: AT5G58060.2 (Arabidopsis thaliana), 5'ss of exon 3
AATACAAGGTCCACTCCCACAATAGAAATGGGCTTTGTGCGGTTGCATTCATGGATGATCATTATCCGGTACGGAGTGCATTTTCTCTTCTGAATCAGgtaccaatcgttatcccctagactcccacttgccttttgcttttggtttaagcccaggttaccaattgtaagctgtagccagtcacttttcattctgttc---
        || ||| |  ||||||||||||| ||||| ||||| |  |||||||| |||||||| || || || ||||| || |||||||| |||||||||  | || ||||     |          ||  | |   |   |  | |  |  | |||  |   |||||  ||       | || ||| ||| |||     
--------GTTCACGCTTACAATAGAAATGGCCTTTGCGCGGTGGGTTTCATGGACGATCATTACCCTGTTCGAAGTGCTTTCTCTCTTCTCAATCAGgtaata-tcattatgttgaaag--------tggttctcaat---gcatcattcgtaagttttc--ctgtaatttgggttgcttgacatttaattttgtctcag

upper sequence: GRMZM2G387076_T02 (Zea mays), 5'ss of exon 3
lower sequence: AT5G58180.1 (Arabidopsis thaliana), 5'ss of exon 2
AATACAAGGTCCACTCCCACAATAGAAATGGGCTTTGTGCGGTTGCATTCATGGATGATCATTATCCGGTACGGAGTGCATTTTCTCTTCTGAATCAGgtaccaatcgttatcccctagactcccacttgccttttgcttttggtttaagcccaggttaccaattgtaagctgtagccagtcacttttcattctgttc
| || || || ||| |  |||| | |||||| || || || || | ||||||||| || |||||||| || || ||||| ||||||||||| |||||||||| || |          | | ||  ||||    |  | | ||| || |||   |   ||    || |     || | || ||  ||||          
AGTATAAAGTGCACGCTTACAACATAAATGGCCTCTGCGCCGTAGGATTCATGGACGACCATTATCCCGTTCGAAGTGCCTTTTCTCTTCTCAATCAGgtacaaaac----------aaaatctaacttctggtacggtcttgtttgaagg--aaaatatt--ttttctttcgttggcattctgtttttgacag----

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|74235349|gb|DT643263.1|DT643263
EST:     TCATGGATGATCATTATCCGGTACGGAGTGCATTTTCTCTTCTGAATCAG                         GTTCTTGATGAGTACCAGAAGGCTTATGGGGACTCCTGGAAATCTGTGACT
genomic: TCATGGATGATCATTATCCGGTACGGAGTGCATTTTCTCTTCTGAATCAGgtaccaatcg ... tttcatgaagGTTCTTGATGAGTACCAGAAGGCTTATGGGGACTCCTGGAAATCTGTGACT
EST: gi|91049820|gb|EB160238.1|EB160238
EST:     TCATGGATGATCATTATCCGGTACGGAGTGCATTTTCTCTTCTGAATCAG                         GTTCTTGATGAGTACCAGAAGGCTTATGGGGACTCCTGGAAATCTGTGACT
genomic: TCATGGATGATCATTATCCGGTACGGAGTGCATTTTCTCTTCTGAATCAGgtaccaatcg ... tttcatgaagGTTCTTGATGAGTACCAGAAGGCTTATGGGGACTCCTGGAAATCTGTGACT
EST: gi|211526464|gb|FL249083.1|FL249083
EST:     TCATGGATGATCATTATCCTGTACGGAGTGCGTTTTCTCTTCTGAATCAG                         GTTCTTGATGAGTACCAGAAGGCTTATGGGGACTCCTGGAAATCTGTGACT
genomic: TCATGGATGATCATTATCCGGTACGGAGTGCATTTTCTCTTCTGAATCAGgtaccaatcg ... tttcatgaagGTTCTTGATGAGTACCAGAAGGCTTATGGGGACTCCTGGAAATCTGTGACT
EST: gi|211526468|gb|FL249087.1|FL249087
EST:     TCATGGATGATCATTATCCTGTACGGAGTGCGTTTTCTCTTCTGAATCAG                         GTTCTTGATGAGTACCAGAAGGCT
genomic: TCATGGATGATCATTATCCGGTACGGAGTGCATTTTCTCTTCTGAATCAGgtaccaatcg ... tttcatgaagGTTCTTGATGAGTACCAGAAGGCT
EST: gi|211529456|gb|FL249093.1|FL249093
EST:     TCATGGATGATCATTATCCTGTACGGAGTGCATTTTCTCTTCTGAATCAG                         GTTCTTGATGAGTACCAGAAGGCTTATGGGGACTCCTGGAAATCTGTGACT
genomic: TCATGGATGATCATTATCCGGTACGGAGTGCATTTTCTCTTCTGAATCAGgtaccaatcg ... tttcatgaagGTTCTTGATGAGTACCAGAAGGCTTATGGGGACTCCTGGAAATCTGTGACT
EST: gi|211526461|gb|FL249080.1|FL249080
EST:     TCATGGATGATCATTATCCGGTACGGAGTGCATTT-CTCTTCTGAATCAG                         GTTCTTGATGAGTACCAGAAGGCTTATGGGGAC
genomic: TCATGGATGATCATTATCCGGTACGGAGTGCATTTTCTCTTCTGAATCAGgtaccaatcg ... tttcatgaagGTTCTTGATGAGTACCAGAAGGCTTATGGGGAC
EST: gi|211529459|gb|FL249096.1|FL249096
EST:     TCATGGATGATCATTATCCTGTACGGAGTGCGTTTTCTCTTCTGAATCAG                         GTTCTTGATGAGTACCAGAAGGCTTATGGGGACTCCTGGAAATCTGTGACT
genomic: TCATGGATGATCATTATCCGGTACGGAGTGCATTTTCTCTTCTGAATCAGgtaccaatcg ... tttcatgaagGTTCTTGATGAGTACCAGAAGGCTTATGGGGACTCCTGGAAATCTGTGACT
EST: gi|211529460|gb|FL249097.1|FL249097
EST:     TCATGGATGATCATTATCCGGTACGGAGTGCATTTTCTCTTCTGAATCAG                         GTTCTTGATGAGTACCAGAAGGCTTATGGGGACTCCTGGAAATCTGTGACT
genomic: TCATGGATGATCATTATCCGGTACGGAGTGCATTTTCTCTTCTGAATCAGgtaccaatcg ... tttcatgaagGTTCTTGATGAGTACCAGAAGGCTTATGGGGACTCCTGGAAATCTGTGACT
EST: gi|60354098|gb|DN221071.1|DN221071
EST:     TCATGGATGATCATTATCCGGTACGGAGTGCATTTTCTCTTCTGAATCAG                         GTTCTTGATGAGTACCAGAAGGCTTATGGGGACTCCTGGAAATCTGTGACT
genomic: TCATGGATGATCATTATCCGGTACGGAGTGCATTTTCTCTTCTGAATCAGgtaccaatcg ... tttcatgaagGTTCTTGATGAGTACCAGAAGGCTTATGGGGACTCCTGGAAATCTGTGACT
EST: gi|211523461|gb|FL249073.1|FL249073
EST:     TCATGGATGATCATTATCCTGTACGGAGTGCGTTTTCTCTTCTGAATCAG                         GTTCTTGATGAGTACCAGAAGGCTTATGGGGACTCCTGGAAATCTGTGACT
genomic: TCATGGATGATCATTATCCGGTACGGAGTGCATTTTCTCTTCTGAATCAGgtaccaatcg ... tttcatgaagGTTCTTGATGAGTACCAGAAGGCTTATGGGGACTCCTGGAAATCTGTGACT
EST: gi|149057998|gb|EE156679.2|EE156679
EST:     TCATGGATGATCATTATCCGGTACGGAGTGCATTTTCTCTTCTGAATCAG                         GTTCTTGATGAGTACCAGAAGGCTTATGGGGACTCCTGGAAATCTGTGACT
genomic: TCATGGATGATCATTATCCGGTACGGAGTGCATTTTCTCTTCTGAATCAGgtaccaatcg ... tttcatgaagGTTCTTGATGAGTACCAGAAGGCTTATGGGGACTCCTGGAAATCTGTGACT
EST: gi|211529454|gb|FL249091.1|FL249091
EST:     TCATGGATGATCATTATCCGGTACGGAGTGCATTTTCTCTTCTGAATCAG                         GTTCTTGATGAGTACCAGAAGGCTTATGGGGACTCCTGGAAATCTGTGACT
genomic: TCATGGATGATCATTATCCGGTACGGAGTGCATTTTCTCTTCTGAATCAGgtaccaatcg ... tttcatgaagGTTCTTGATGAGTACCAGAAGGCTTATGGGGACTCCTGGAAATCTGTGACT
EST: gi|211529452|gb|FL249089.1|FL249089
EST:     TCATGGATGATCATTATCCGGTACGGAGTGCATTTTCTCTTCTGAATCAG                         GTTCTTGATGAGTACCAGAAGGCTTATGGGGACTCCTGGAAATCTGTGACT
genomic: TCATGGATGATCATTATCCGGTACGGAGTGCATTTTCTCTTCTGAATCAGgtaccaatcg ... tttcatgaagGTTCTTGATGAGTACCAGAAGGCTTATGGGGACTCCTGGAAATCTGTGACT
EST: gi|211526469|gb|FL249088.1|FL249088
EST:     TCATGGATGATCATTATCCGGTACGGAGTGCATTTTCTCTTCTGAATCAG                         GTTCTTGATGAGTACCAGAAGGCTTATGGGGACTCCTGGAAATCTGTGACT
genomic: TCATGGATGATCATTATCCGGTACGGAGTGCATTTTCTCTTCTGAATCAGgtaccaatcg ... tttcatgaagGTTCTTGATGAGTACCAGAAGGCTTATGGGGACTCCTGGAAATCTGTGACT
EST: gi|44681914|gb|CK786962.1|CK786962
EST:     TCATGGATGATCATTATCCTGTACGGAGTGCATTTTCTCTTCTGAATCAG                         GTTCTTGATGAGTACCAGAAGGCTTATGGGGACTCCTGGAAATCTGTGACT
genomic: TCATGGATGATCATTATCCGGTACGGAGTGCATTTTCTCTTCTGAATCAGgtaccaatcg ... tttcatgaagGTTCTTGATGAGTACCAGAAGGCTTATGGGGACTCCTGGAAATCTGTGACT

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: 46 (upstream exon), 48 (downstream exon)
Score: 57

AATACAAGGTCCACTCCCACAATAGAAATGGGCTTTGTGCGGTTGCATTCATGGATGATCATTATCCGGTACGGAGTGCATTTTCTCTTCTGAATCAGgtaccaatcg ... tttcatgaagGTTCTTGATGAGTACCAGAAGGCTTATGGGGACTCCTGGAAATCTGTGACTGCAGATGAAACTCAACAGTGGGCTTTCCTGACAGACGCCTTGACAAAAT


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 108

AATACAAGGTCCACTCCCACAATAGAAATGGGCTTTGTGCGGTTGCATTCATGGATGATCATTATCCGGTACGGAGTGCATTTTCTCTTCTGAATCAGgtaccaatcg ... tttcatgaagGTTCTTGATGAGTACCAGAAGGCTTATGGGGACTCCTGGAAATCTGTGACTGCAGATGAAACTCAACAGTGGGCTTTCCTGACAGACGCCTTGACAAAAT


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 88

AATACAAGGTCCACTCCCACAATAGAAATGGGCTTTGTGCGGTTGCATTCATGGATGATCATTATCCGGTACGGAGTGCATTTTCTCTTCTGAATCAGgtaccaatcg ... tttcatgaagGTTCTTGATGAGTACCAGAAGGCTTATGGGGACTCCTGGAAATCTGTGACTGCAGATGAAACTCAACAGTGGGCTTTCCTGACAGACGCCTTGACAAAAT


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 71

AATACAAGGTCCACTCCCACAATAGAAATGGGCTTTGTGCGGTTGCATTCATGGATGATCATTATCCGGTACGGAGTGCATTTTCTCTTCTGAATCAGgtaccaatcg ... tttcatgaagGTTCTTGATGAGTACCAGAAGGCTTATGGGGACTCCTGGAAATCTGTGACTGCAGATGAAACTCAACAGTGGGCTTTCCTGACAGACGCCTTGACAAAAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATACAAGGTCCACTCCCACAATAGAAATGGGCTTTGTGCGGTTGCATTCATGGATGATCATTATCCGGTACGGAGTGCATTTTCTCTTCTGAATCAGgtaccaatcgttatcccctagactcccacttgccttttgcttttggtttaagcccaggttaccaattgtaagctgtagccagtcacttttcattctgttc

- - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actcccac