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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAAgtaagtatctcaaggaacgttttagctatagggaaatgtcactgacttatggttatccaaacttttaacattctcattctattgaaataatataaaagga...

Basic information

species Zea mays
transcript GRMZM5G825110_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G825110_T02 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os01g55360.1 (Oryza sativa), 5'ss of exon 10
GATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAAgtaagta-tctcaaggaacgttttagctatagggaaatgtcactgacttatggttatccaaacttttaacat-----tctcattctattgaaataatataaaagga
|||||||| ||||||||||||||||||||||| ||||||||  |||||||||| || ||||||| |||| | |||  || ||  |||| | ||||||||||| |       ||| || || | | | |      | |  ||||||  | ||| | ||      
GATTTTGGAGACAGCATACCTGGGCATGGTGGGATTACTGACCGAATGGATTGTCAGgtaagtaatctcgaagaatattctaattataagaaaatgtcactgcccatataatatacatacatatgaaagcgatatgtgtttctatatacatattgta------

upper sequence: GRMZM5G825110_T02 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA10G32660.1 (Glycine max), 5'ss of exon 9
-------------------------------------------GATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAAgtaagtatctcaaggaacgttttagctatagggaaatgtcactgacttatggttatccaaacttttaacattctcattctattgaaataatataaaagga-----
                                           || |||||||| || || || || |||||||||||||| || |||||||||||||| |||  |   |      | |||  |    ||   |  | |   | | | ||   |||  ||    | |  | ||| ||  | ||       | |   |        
GGTCAGGTAGAAACAGACTTGCTGTGTGTTTCCATTTTTGCAGGACTTTGGTGATAGTATTCCGGGACATGGTGGAATTACCGACAGAATGGATTGCCAGgtagattcttttg---atgttgcaatc-tacaaatttatt-ttaaatcattaatatttaactactcaggactcttatgtttttttgtccttgtgggaaactttta

upper sequence: GRMZM5G825110_T02 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA02G46440.1 (Glycine max), 5'ss of exon 10
GATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAAgtaagtatctcaaggaacgttttagctatagggaaatgtcactgacttatggttatccaaacttttaacattctcattctattgaaataatataaaagga------
|| ||||||||||| |||||||| ||||||||| |||| || |||||||| ||||| ||  |    |  |      | |     |    ||| | ||  ||  ||||   |    |  || |     |||||| | ||  || | | | || |          
GACTTTGGTGACAGTATACCTGGACATGGTGGATTTACAGACAGAATGGACTGCCAGgtttgctcatagatatttatgtactagaataagaattatccttggtttatatctgaataggctat-----ttctcaat-taaggatacactttacagattttttat

upper sequence: GRMZM5G825110_T02 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA10G32660.2 (Glycine max), 5'ss of exon 10
GATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAAgtaagtatctcaaggaacgttttagctatagggaaatgtcactgacttatggttatccaaacttttaacattctcattctattgaaataatataaaagga-----
|| |||||||| || || || || |||||||||||||| || |||||||||||||| |||  |   |      | |||  |    ||   |  | |   | | | ||   |||  ||    | |  | ||| ||  | ||       | |   |        
GACTTTGGTGATAGTATTCCGGGACATGGTGGAATTACCGACAGAATGGATTGCCAGgtagattcttttg---atgttgcaatc-tacaaatttatt-ttaaatcattaatatttaactactcaggactcttatgtttttttgtccttgtgggaaactttta

upper sequence: GRMZM5G825110_T02 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA20G34940.1 (Glycine max), 5'ss of exon 10
GATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAAgtaagtatctcaaggaacgttttagctatagggaaatgtcactgacttatggttatccaaactttta-acattctcattctattgaaataatataaaagga---
||||||||||| || || || || |||||||||||||| || |||||||||||||| |||  |   |      | |||  |    ||   |  | |     |    |   ||        | ||  | || |  | ||  ||    | | | ||       
GATTTTGGTGATAGTATTCCAGGACATGGTGGAATTACCGACAGAATGGATTGCCAGgtagattcttttg---atgttacaatc-tacaaatttattttcaatcattaactacttgggactctatgcttttttgtccttgtggggaacttttaatcatcat

upper sequence: GRMZM5G825110_T02 (Zea mays), 5'ss of exon 10
lower sequence: AT4G26770.1 (Arabidopsis thaliana), 5'ss of exon 9
GATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAAgtaagtatctcaaggaacgttttagctatagggaaatgtcactgacttatggttatccaaacttttaacattctcattctattgaaataatataaaagga
||||| || ||||||||||| || ||||| ||| ||||||| ||||||||||||||||||||  || | |   ||||   |     || | ||| | |       || ||  |  ||||    ||  || |      | || |              
GATTTCGGAGACAGCATACCAGGACATGGAGGATTTACTGACAGAATGGATTGCCAAgtaagagtcacta---acgtcgaaa----agtgcaatatgatctttgcatcgt--tttaaac---gaatcttgttgcctaaatgcag-------------

upper sequence: GRMZM5G825110_T02 (Zea mays), 5'ss of exon 10
lower sequence: Vv19s0090g01220.t01 (Vitis vinifera), 5'ss of exon 9
GATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAAgtaagt----atctcaaggaacgttttagctatagggaa-atgtcactgacttatggttatccaaacttttaacattctcattctattgaaataatataaaagga
|||||||| || || || ||||| |||||||||||||| || ||||||||||| || |||||     |  |     |  | ||||   ||||  |  ||||   |   | ||  || |  ||  | |||   ||  |||||     ||| |  |    |   
GATTTTGGAGATAGTATTCCTGGACATGGTGGAATTACAGACAGAATGGATTGTCAGgtaagatagaaaattttatactgatttattcatagtaatcatgtttttttatcatcattgtttaa--tgttattcttgacattcccacaaaaaaccacgtca---

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|32806967|gb|CD959201.1|CD959201
EST:     GTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAA                         ATGGTTATGGCAGTGTTTGCATACATATACCACCAGTCATTCATTGCACCT
genomic: GTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAAgtaagtatct ... ttttccccagATGGTTATGGCAGTGTTTGCATACATATACCACCAGTCATTCATTGCACCT
EST: gi|32809742|gb|CD961976.1|CD961976
EST:     GTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAA                         ATGGTTATGGCAGTGTTTGCATACATATACCACCAGTCATTCATTGCACCT
genomic: GTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAAgtaagtatct ... ttttccccagATGGTTATGGCAGTGTTTGCATACATATACCACCAGTCATTCATTGCACCT
EST: gi|78079229|gb|DV507641.1|DV507641
EST:     CATACCTGGGCATGGGGGAATTACTGATAGAATGGATTGCCAA                         ATGGTTATGGCAGTGTTTGCATACATATACCACCAGTCATTCATTGCACCT
genomic: CATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAAgtaagtatct ... ttttccccagATGGTTATGGCAGTGTTTGCATACATATACCACCAGTCATTCATTGCACCT
EST: gi|71760475|gb|DR958412.1|DR958412
EST:     GTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAA                         ATGGTTATGGCAGTGTTTGCATACATATACCACCAGTCATTCATTGCACCT
genomic: GTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAAgtaagtatct ... ttttccccagATGGTTATGGCAGTGTTTGCATACATATACCACCAGTCATTCATTGCACCT
EST: gi|71426533|gb|DR807583.1|DR807583
EST:     GTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAA                         ATGGTTATGGCAGTGTTTGCATACATATACCACCAGTCATTCATTGCACCT
genomic: GTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAAgtaagtatct ... ttttccccagATGGTTATGGCAGTGTTTGCATACATATACCACCAGTCATTCATTGCACCT
EST: gi|78121240|gb|DV539624.1|DV539624
EST:     GTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAA                         ATGGTTATGGCAGTGTTTGCATACATATACCCCCAGTCATTCATTGCACCT
genomic: GTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAAgtaagtatct ... ttttccccagATGGTTATGGCAGTGTTTGCATACATATACCACCAGTCATTCATTGCACCT
EST: gi|71426082|gb|DR807132.1|DR807132
EST:     GTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAA                         ATGGTTATGGCAGTGTTTGCATACATATACCACCAGTCATTCATTGCACCT
genomic: GTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAAgtaagtatct ... ttttccccagATGGTTATGGCAGTGTTTGCATACATATACCACCAGTCATTCATTGCACCT
EST: gi|60338336|gb|DN205309.1|DN205309
EST:     GTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAA                         ATGGTTATGGCAGTGTTTGCATACATATACCACCAGTCATTCATTGCACCT
genomic: GTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAAgtaagtatct ... ttttccccagATGGTTATGGCAGTGTTTGCATACATATACCACCAGTCATTCATTGCACCT
EST: gi|60344634|gb|DN211607.1|DN211607
EST:     GTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAA                         ATGGTTATGGCAGTGTTTGCATACATATACCACCAGTCATTCATTGCACCT
genomic: GTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAAgtaagtatct ... ttttccccagATGGTTATGGCAGTGTTTGCATACATATACCACCAGTCATTCATTGCACCT
EST: gi|76014866|gb|DT942036.1|DT942036
EST:     GTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAA                         ATGGTTATGGCAGTGTTTGCATACATATACCACCAGTCATTCATTGCACCT
genomic: GTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAAgtaagtatct ... ttttccccagATGGTTATGGCAGTGTTTGCATACATATACCACCAGTCATTCATTGCACCT
EST: gi|76021500|gb|DT948670.1|DT948670
EST:     GTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAA                         ATGGTTATGGCAGTGTTTGCATACATATACCACCAGTCATTCATTGCACCT
genomic: GTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAAgtaagtatct ... ttttccccagATGGTTATGGCAGTGTTTGCATACATATACCACCAGTCATTCATTGCACCT
EST: gi|76287485|gb|DV027053.1|DV027053
EST:     GTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAA                         ATGGTTATGGCAGTGTTTGCATACATATACCACCAGTCATTCATTGCACCT
genomic: GTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAAgtaagtatct ... ttttccccagATGGTTATGGCAGTGTTTGCATACATATACCACCAGTCATTCATTGCACCT
EST: gi|7135092|gb|AW497912.1|AW497912
EST:     GTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAA                         ATGGTTATGGCAGTGTTTGCATACATATACCACCAGTCATTCATTGCACCT
genomic: GTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAAgtaagtatct ... ttttccccagATGGTTATGGCAGTGTTTGCATACATATACCACCAGTCATTCATTGCACCT

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: 91

GATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAAgtaagtatct ... ttttccccagATGGTTATGGCAGTGTTTGCATACATATACCACCAGTCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 99

GATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAAgtaagtatct ... ttttccccagATGGTTATGGCAGTGTTTGCATACATATACCACCAGTCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 126

GATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAAgtaagtatct ... ttttccccagATGGTTATGGCAGTGTTTGCATACATATACCACCAGTCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 79

GATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAAgtaagtatct ... ttttccccagATGGTTATGGCAGTGTTTGCATACATATACCACCAGTCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAAgtaagtatctcaaggaacgttttagctatagggaaatgtcactgacttatggttatccaaacttttaacattctcattctattgaaataatataaaagga

- - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - -  GGTGGA