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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTGGCTGCCATTCCATGGTTCATTGGAGCTTTCGTTCTTATATGTGTGCGGGTACATGACCAACGAGAGAAACCAGGATACGTTGCTTGCACAATTGCTgtaagttcctttctattaatacaatgcaaccctgctgctcatttgtttacctttggaatttgagattgagctgcatggaactgtggaagcaaactgtttg...

Basic information

species Zea mays
transcript GRMZM2G022453_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G022453_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os05g49020.1 (Oryza sativa), 5'ss of exon 3
CTTGGCTGCCATTCCATGGTTCATTGGAGCTTTCGTTCTTATATGTGTGCGGGTACATGACCAACGAGAGAAACCAGGATACGTTGCTTGCACAATTGCTgtaagttcctttctattaatacaatgcaaccctgctgct-catttgtttacctttggaatttg-agattgagctgcatggaactgtggaagcaaactgtttg
| | |||||||| |||||||   |||| |||||| | || |||||||| || ||||||||| |  |||||||||||||||| ||||| |||||  |||||||||||   |||||| | || |  ||||| |    || |  |||      || |   ||  || || |    |||  |   | | ||||    || |     
CCTTGCTGCCATCCCATGGTATGTTGGGGCTTTCATACTAATATGTGTCCGAGTACATGACTACAGAGAGAAACCAGGATATGTTGCCTGCACTGTTGCTgtaagtatatttctactgatgcgctgcaatcacattgttatattctccctccgtcacaaaatgtagctatttctggctaagaatctggatcagaaatagc--

upper sequence: GRMZM2G022453_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv19s0135g00070.t01 (Vitis vinifera), 5'ss of exon 3
---CTTGGCTGCCATTCCATGGTTCATTGGAGCTTTCGTTCTTATATGTGTGCGGGTACATGACCAACGAGAGAAACCAGGATACGTTGCTTGCACAATTGCTgtaagtt--cctttctattaatacaatgcaaccctgctgctcatttgtttacctttggaatttgagattgagctgcatggaac-tgtggaagcaaactgtttg
   | | |||||  | || ||||   ||||    ||| ||||  | ||||   | |||   ||| |  ||||||||||||| ||| |||| |||||||||||||| |||   | ||  |  | ||   ||   | | |  ||   |  ||||||    |    |||     || |     | |  |   |  |||     |  |  
CTTCCTTGCTGCTGTCCCCTGGTATGTTGGGTTCTTCCTTCTACTTTGTGCCAGAGTA---GACTACAGAGAGAAACCAGGCTACATTGCCTGCACAATTGCTgtgagtaaactttattgctcatttgattttaactttatgga-agatgtttagtgcttacttttccacctgtgtcttctcgttcacctttaagttttgtaat--
















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|5761881|gb|AI966854.1|AI966854
EST:     GGGTACATGACCAACGAGAGAAACCAGGATACGTTGCTTGCACAATTGCT                         GCCGTTGTTGCTGCCGTTGCCATCCTCTTGGGGGTAACTNNNNNNNNGCAC
genomic: GGGTACATGACCAACGAGAGAAACCAGGATACGTTGCTTGCACAATTGCTgtaagttcct ... gctgtggcagGCCGTTGTTGCTGCCGTTGCCATCCTCTTGGGGGTAACTAAAGGAACGCAC
EST: gi|211021435|gb|FL345703.1|FL345703
EST:     GGGTACATGACCAACGAGAGAAACCAGGATACGTTGCTTGCACAATTGCT                         GCCGTTGTTGCTGCCGTTGCCATCCTCTTGGGGG-AACTAAAGGAACGCAC
genomic: GGGTACATGACCAACGAGAGAAACCAGGATACGTTGCTTGCACAATTGCTgtaagttcct ... gctgtggcagGCCGTTGTTGCTGCCGTTGCCATCCTCTTGGGGGTAACTAAAGGAACGCAC
EST: gi|89248089|gb|DY619875.1|DY619875
EST:     GGGTACATGACCAACGAGAGAAACCAGGATACGTTGCTTGCACAATTGCT                         GCCGTTGTTGCTGCCGTTGCCATCCTCTTGGGGGTAACTAAAGGAACGCAC
genomic: GGGTACATGACCAACGAGAGAAACCAGGATACGTTGCTTGCACAATTGCTgtaagttcct ... gctgtggcagGCCGTTGTTGCTGCCGTTGCCATCCTCTTGGGGGTAACTAAAGGAACGCAC
EST: gi|211349709|gb|FL339346.1|FL339346
EST:     GGGTACATGACCAACGAGAGAAACCAGGATACGTTGCTTGCACCATTGCT                         GCCGTTGTTGCTGCCGTTGCCATCCTCCTGGGG
genomic: GGGTACATGACCAACGAGAGAAACCAGGATACGTTGCTTGCACAATTGCTgtaagttcct ... gctgtggcagGCCGTTGTTGCTGCCGTTGCCATCCTCTTGGGG
EST: gi|60397723|gb|DN230539.1|DN230539
EST:     GGGTACATGACCAACGAGAGAAACCAGTATACGTTGCTTGCACAATTGCT                         GCCGTTGTTGCTGCCGTTGCCATCCTCTTGGGGGTAAATAAAGGAACGCAC
genomic: GGGTACATGACCAACGAGAGAAACCAGGATACGTTGCTTGCACAATTGCTgtaagttcct ... gctgtggcagGCCGTTGTTGCTGCCGTTGCCATCCTCTTGGGGGTAACTAAAGGAACGCAC
EST: gi|89248090|gb|DY619876.1|DY619876
EST:     GGGTACATGACCAACGAGAGAAACCAGGATACGTTGCTTGCACAATTGCT                         GCCGTTGTTGCTGCCGTTGCCATCCTCTTGGGGGTAACTAAAGGAACGCAC
genomic: GGGTACATGACCAACGAGAGAAACCAGGATACGTTGCTTGCACAATTGCTgtaagttcct ... gctgtggcagGCCGTTGTTGCTGCCGTTGCCATCCTCTTGGGGGTAACTAAAGGAACGCAC
EST: gi|166480193|gb|EG064186.1|EG064186
EST:     AACGAGAGAAACCAGGATACGTTGCTTGCACAATTGCT                         GCCGTTGTTGCTGCCGTTGCCATCCTCCTGGGGGTAACTAAAGGAACGCAC
genomic: AACGAGAGAAACCAGGATACGTTGCTTGCACAATTGCTgtaagttcct ... gctgtggcagGCCGTTGTTGCTGCCGTTGCCATCCTCTTGGGGGTAACTAAAGGAACGCAC
EST: gi|149085931|gb|EE175459.2|EE175459
EST:     GGGTACATGACCAACGAGAGAAACCAGGATACGTTGCTTGCACAATTGCT                         GCCGTTGTTGCTGCCGTTGCCATCCTCTTGGGGGTAACTAAAGGAACGCAC
genomic: GGGTACATGACCAACGAGAGAAACCAGGATACGTTGCTTGCACAATTGCTgtaagttcct ... gctgtggcagGCCGTTGTTGCTGCCGTTGCCATCCTCTTGGGGGTAACTAAAGGAACGCAC
EST: gi|110519086|gb|EE023673.1|EE023673
EST:     GGGTACATGACCAACGAGAGAAACCAGGATACGTTGCTTGCACAATTGCT                         GCCGTTGTTGCTGCCGTTGCCATCCTCTTGGGGGTAACTAAAGGAACGCAC
genomic: GGGTACATGACCAACGAGAGAAACCAGGATACGTTGCTTGCACAATTGCTgtaagttcct ... gctgtggcagGCCGTTGTTGCTGCCGTTGCCATCCTCTTGGGGGTAACTAAAGGAACGCAC

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: 67

CTTGGCTGCCATTCCATGGTTCATTGGAGCTTTCGTTCTTATATGTGTGCGGGTACATGACCAACGAGAGAAACCAGGATACGTTGCTTGCACAATTGCTgtaagttcct ... gctgtggcagGCCGTTGTTGCTGCCGTTGCCATCCTCTTGGGGGTAACTAAAGGAACGCACGTGTGGTGAATTGCCTCCAGAGAAGGCAATCAATGTGTATTTGCGTTGT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 50

CTTGGCTGCCATTCCATGGTTCATTGGAGCTTTCGTTCTTATATGTGTGCGGGTACATGACCAACGAGAGAAACCAGGATACGTTGCTTGCACAATTGCTgtaagttcct ... gctgtggcagGCCGTTGTTGCTGCCGTTGCCATCCTCTTGGGGGTAACTAAAGGAACGCACGTGTGGTGAATTGCCTCCAGAGAAGGCAATCAATGTGTATTTGCGTTGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 64

CTTGGCTGCCATTCCATGGTTCATTGGAGCTTTCGTTCTTATATGTGTGCGGGTACATGACCAACGAGAGAAACCAGGATACGTTGCTTGCACAATTGCTgtaagttcct ... gctgtggcagGCCGTTGTTGCTGCCGTTGCCATCCTCTTGGGGGTAACTAAAGGAACGCACGTGTGGTGAATTGCCTCCAGAGAAGGCAATCAATGTGTATTTGCGTTGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 62

CTTGGCTGCCATTCCATGGTTCATTGGAGCTTTCGTTCTTATATGTGTGCGGGTACATGACCAACGAGAGAAACCAGGATACGTTGCTTGCACAATTGCTgtaagttcct ... gctgtggcagGCCGTTGTTGCTGCCGTTGCCATCCTCTTGGGGGTAACTAAAGGAACGCACGTGTGGTGAATTGCCTCCAGAGAAGGCAATCAATGTGTATTTGCGTTGT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTGGCTGCCATTCCATGGTTCATTGGAGCTTTCGTTCTTATATGTGTGCGGGTACATGACCAACGAGAGAAACCAGGATACGTTGCTTGCACAATTGCTgtaagttcctttctattaatacaatgcaaccctgctgctcatttgtttacctttggaatttgagattgagctgcatggaactgtggaagcaaactgtttg

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