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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTATTGAGAGAGCATATGGATGCAAGCTGTGTATTGGGCCTTGCACCACAAGAGGGGAGgtatgaaaatgatataaagatcaccagcttaaagcttaatgaattttgtgtaaccatcttctgtgttgttgagctgttttctaaagtgtttccacttaacatcctaag

Basic information

species Zea mays
transcript GRMZM2G553314_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G553314_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os08g19850.1 (Oryza sativa), 5'ss of exon 3
TCTATTGAGAGAGCATATGGATGCAAGCTGTGTATTGGGCCTTGCACCACAAGAGGGGAGgtatgaaaatgatataaagatcaccagcttaaagcttaatgaattttgtgtaaccatcttctgtgttgttgagctgttttctaaagtgtttccacttaacatcctaag
||| ||||||| |||||||| |||||||||||||||||||| || || ||||||||||||||||  || | ||  ||| |||    | | |  ||   |   ||  |  |       | |||  ||  || |  |  | | |  | | || ||  ||||         
TCTCTTGAGAGGGCATATGGCTGCAAGCTGTGTATTGGGCCATGTACTACAAGAGGGGAGgtattgaattaat-caaaaatcgt--gttcagtgcaagaaagataataagc------cctcttagtgattaacataatgtttctacttttacctgttaag--------

upper sequence: GRMZM2G553314_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA01G03930.1 (Glycine max), 5'ss of exon 2
TCTATTGAGAGAGCATATGGATGCAAGCTGTGTATTGGGCCTTGCACCACAAGAGGGGAGgtatgaaaatgatataaagatcaccagcttaaagct-taatgaattttgtgtaaccatcttctgtgttgttgagctgttttctaaagtgtttccacttaacatcctaag----
||  ||||||  |  |||||||||||| | || |||||||||||||| |||||||| ||||| ||    || | |     |       |||| |   |  ||   | | |||   | |||  |||| ||||    ||| |  | |  | |    | | ||  |  |       
TCACTTGAGACGGAGTATGGATGCAAGTTATGCATTGGGCCTTGCACTACAAGAGGAGAGgtttgtgtgtgttttt----tttttgttttaatgtgattgtgggctgtttgttgtc-tctgttgtgatgtttttgtgtgtattga--tatagaaagtgaatgtttttgtttag

upper sequence: GRMZM2G553314_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA02G03750.1 (Glycine max), 5'ss of exon 2
TCTATTGAGAGAGCATATGGATGCAAGCTGTGTATTGGGCCTTGCACCACAAGAGGGGAGgtatgaaaatgatataaagatc---accagcttaaagcttaatgaattttgtgtaaccatcttctgtgt-tgttgagctgttttctaaagtgtttccacttaacatcctaag
||  ||||||  |  |||||||||||||| || |||||||||||||| |||||||| ||||| ||    |    |     |    ||  | ||   |  |  ||| | |  ||| |   | || ||||| | ||||  |      | ||  ||||    |||          
TCACTTGAGACGGAGTATGGATGCAAGCTCTGCATTGGGCCTTGCACTACAAGAGGAGAGgtttgtgtgtaccttttttgttttaacgtgtttgcggactgttgactctgttgtgat-gttttgtgtgtgtattgaaatagaaagtgaa-cgtttttgtttag---------

upper sequence: GRMZM2G553314_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv19s0015g00470.t01 (Vitis vinifera), 5'ss of exon 3
TCTATTGAGAGAGCATATGGATGCAAGCTGTGTATTGGGCCTTGCACCACAAGAGGGGAGgtatgaaaatgatataaagatcaccagcttaaagcttaatgaattttgt-gtaaccatcttctgtgttgttgagctgttttctaaagtgttt---ccacttaacatcctaag
 |  |||| |  | |||||| ||||||||||| |||||||| || ||||||||||| ||||||||       |||||  || |  || ||       |   ||| |  | || |   | |  | | || || |  | || |      |||||     | || || | ||   
GCCCTTGAAATGGAATATGGTTGCAAGCTGTGCATTGGGCCCTGTACCACAAGAGGAGAGgtatgt------tataagcatgattagttttgga---agccaatctgattgtgatgttttcttattttatttaaatattattatttttgtttaattaattttaccttct---

upper sequence: GRMZM2G553314_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv01s0026g00340.t01 (Vitis vinifera), 5'ss of exon 3
TCTATTGAGAGAGCATATGGATGCAAGCTGTGTATTGGGCCTTGCACCACAAGAGGGGAGgtatgaaaatgatataaagatcaccagcttaaagcttaatgaattttgtgtaaccatcttctgtgttgttgagctgttttctaaagtgtttccacttaacatcctaag
 |  ||||    |||||||| |||||  |||| |||||||| || ||||||||||| ||||||||  |     ||    |      |     |   | || |   || | |     |  | |    | || |  | || | |||    ||||  |||           
GCCCTTGAAGTGGCATATGGTTGCAAATTGTGCATTGGGCCCTGTACCACAAGAGGAGAGgtatgttataagcatgtttagttttggaagctaatctgattaccatttttttcatgttgttttaaatattaattttttgtttaattaatttcaccttctt--------

upper sequence: GRMZM2G553314_T01 (Zea mays), 5'ss of exon 3
lower sequence: PP1S400_36V6.1 (Physcomitrella patens), 5'ss of exon 4
TCTATTGAGAGAGCATATGGATGCAAGCTGTGTATTGGGCCTTGCACCACAAGAGGGGAGgtatgaaaatgatataaagatcaccagcttaaagcttaatgaattttgtgtaaccatcttctgtgttgttgagctgttttctaaagtgtttccacttaacatcctaag
|| ||||| |   |||| ||||||||||| || ||||| ||||||||||| ||||| ||||||   || |    ||    || |         | ||  ||  |   ||  |  |    | | |  || |  |  |||| || |  || || | ||||||        
TCAATTGAAATGACATACGGATGCAAGCTTTGCATTGGACCTTGCACCACTAGAGGAGAGgtaccgaatttggctac---tccctctgccgttgatt--tgggtgccgtaaagtctctgtttttcgtgcttcgtcgtttgctca--tgatttctcttaactattcgc-

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|76021644|gb|DT948814.1|DT948814
EST:     GAGCATATGGATGCAAGCTGTGTATTGGGCCTTGCACCACAAGAGGGGAG                         GGTTTCTACTATGATGCTTACTACAATGATCAGACATTGAATGAGGAGCAC
genomic: GAGCATATGGATGCAAGCTGTGTATTGGGCCTTGCACCACAAGAGGGGAGgtatgaaaat ... acatcctaagGGTTTCTACTATGATGCTTACTACAATGATCAGACATTGAATGAGGAGCAC
EST: gi|149089740|gb|EE179011.2|EE179011
EST:     GAGCATATGGATGCAAGCTGTGTATTGGGCCTTGCACCACAAGAGGGGAG                         GGTTTCTACTATGATGCTTACTACAATGATCAGACATTGAATGAGGAGCAC
genomic: GAGCATATGGATGCAAGCTGTGTATTGGGCCTTGCACCACAAGAGGGGAGgtatgaaaat ... acatcctaagGGTTTCTACTATGATGCTTACTACAATGATCAGACATTGAATGAGGAGCAC
EST: gi|22819104|gb|BU499194.1|BU499194
EST:     CACCACAAGAGGGGAG                         GGTTTCTACTATGATGCTTACTACAATGATCAGACATTGAATGAGGAGCAC
genomic: CACCACAAGAGGGGAGgtatgaaaat ... acatcctaagGGTTTCTACTATGATGCTTACTACAATGATCAGACATTGAATGAGGAGCAC
EST: gi|26457084|gb|CA828667.1|CA828667
EST:     TTGCACCACAAGAGGGGAG                         GGTTTCTACTATGATGCTTACTACAATGATCAGACATTGAATGAGGAGCAC
genomic: TTGCACCACAAGAGGGGAGgtatgaaaat ... acatcctaagGGTTTCTACTATGATGCTTACTACAATGATCAGACATTGAATGAGGAGCAC
EST: gi|211033167|gb|FL324568.1|FL324568
EST:     GAGCATATGGATGCAAGCTGTGTATTGGGCCTTGCACCACAAGAGGGGAG                         GGTTTCTACTATGATGCTTACTACAATGATCAGACATTGAATGAGGAGCAC
genomic: GAGCATATGGATGCAAGCTGTGTATTGGGCCTTGCACCACAAGAGGGGAGgtatgaaaat ... acatcctaagGGTTTCTACTATGATGCTTACTACAATGATCAGACATTGAATGAGGAGCAC
EST: gi|50334018|gb|CO529144.1|CO529144
EST:     GAGCATATGGATGCAAGCTGTGTATTGGGCCTTGCACCACAAGAGGGGAG                         GGTTTCTACTATGATGCTTACTACAATGATCAGACATTGAATGANGAGCAC
genomic: GAGCATATGGATGCAAGCTGTGTATTGGGCCTTGCACCACAAGAGGGGAGgtatgaaaat ... acatcctaagGGTTTCTACTATGATGCTTACTACAATGATCAGACATTGAATGAGGAGCAC
EST: gi|50334514|gb|CO529640.1|CO529640
EST:     CTTGCACCACAAGAGGGGAG                         GGTTTCTACTATGATGCTTACTACAATGATCAGACATTGAATGAGGAGCAC
genomic: CTTGCACCACAAGAGGGGAGgtatgaaaat ... acatcctaagGGTTTCTACTATGATGCTTACTACAATGATCAGACATTGAATGAGGAGCAC
EST: gi|211514340|gb|FL308803.1|FL308803
EST:     GAGCATATGGATGCAAGCTGTGTATTGGGCCTTGCACCACAAGAGGGGAG                         GGTTTCTACTATG
genomic: GAGCATATGGATGCAAGCTGTGTATTGGGCCTTGCACCACAAGAGGGGAGgtatgaaaat ... acatcctaagGGTTTCTACTATG
EST: gi|78092217|gb|DV520591.1|DV520591
EST:     GAGCATATGGATGCAAGCTGTGTATTGGGCCTTGCACCACAAGAGGGGAG                         GGTTTCTACTATGATGCTTACTACAATGATCAGACATTGAATGAGGAGCAC
genomic: GAGCATATGGATGCAAGCTGTGTATTGGGCCTTGCACCACAAGAGGGGAGgtatgaaaat ... acatcctaagGGTTTCTACTATGATGCTTACTACAATGATCAGACATTGAATGAGGAGCAC

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), 48 (downstream exon)
Score: 273

TCTATTGAGAGAGCATATGGATGCAAGCTGTGTATTGGGCCTTGCACCACAAGAGGGGAGgtatgaaaat ... acatcctaagGGTTTCTACTATGATGCTTACTACAATGATCAGACATTGAATGAGGAGCACTTTGGTATCATTGAAAACCAAGCTAAAAAGGCTGTTGCG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 151

TCTATTGAGAGAGCATATGGATGCAAGCTGTGTATTGGGCCTTGCACCACAAGAGGGGAGgtatgaaaat ... acatcctaagGGTTTCTACTATGATGCTTACTACAATGATCAGACATTGAATGAGGAGCACTTTGGTATCATTGAAAACCAAGCTAAAAAGGCTGTTGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 119

TCTATTGAGAGAGCATATGGATGCAAGCTGTGTATTGGGCCTTGCACCACAAGAGGGGAGgtatgaaaat ... acatcctaagGGTTTCTACTATGATGCTTACTACAATGATCAGACATTGAATGAGGAGCACTTTGGTATCATTGAAAACCAAGCTAAAAAGGCTGTTGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 134

TCTATTGAGAGAGCATATGGATGCAAGCTGTGTATTGGGCCTTGCACCACAAGAGGGGAGgtatgaaaat ... acatcctaagGGTTTCTACTATGATGCTTACTACAATGATCAGACATTGAATGAGGAGCACTTTGGTATCATTGAAAACCAAGCTAAAAAGGCTGTTGCG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTATTGAGAGAGCATATGGATGCAAGCTGTGTATTGGGCCTTGCACCACAAGAGGGGAGgtatgaaaatgatataaagatcaccagcttaaagcttaatgaattttgtgtaaccatcttctgtgttgttgagctgttttctaaagtgtttccacttaacatcctaag

- - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG