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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctcctactgtttgctctctgcaattttattcaatcaactccatttggtactgtaattgtaatgctgctcaacctgtaatggctagGATGACAATGGTAACTTGTTGGTTACCGAGTATGGAATGTGTGAATACAAGGATCACCAGACATTGTCCATGCAAGAAGTGCCTGAAAATTCTGCACCTG

Basic information

species Zea mays
transcript GRMZM2G100639_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G100639_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g39850.1 (Oryza sativa), 3'ss of exon 4
gtatgctcctactgtttgctctctgcaattttattcaatcaactccatttggtactgtaattgtaatgctgctcaacctgtaatggctagGATGACAATGGTAACTTGTTGGTTACCGAGTATGGAATGTGTGAATACAAGGATCACCAGACATTGTCCATGCAAGAAGTGCCTGAAAATTCTGCACCTG
|||   || |    |   |  | ||| | | |||||||| ||  | ||||| |  | |  ||||||||||||| ||  || |||   |||||||| ||||||||||||||||| || ||||| || ||||||||||||||||||||||| ||| | ||||||||||||||||||||||||||||| ||||
gtacattcttttgatcatccttttgctactctattcaatgaaacctatttgttgttttgtttgtaatgctgct-aatttggaatacttagGATGAAAATGGTAACTTGTTGGTCACTGAGTACGGGATGTGTGAATACAAGGATCACCAAACACTCTCCATGCAAGAAGTGCCTGAAAATTCTGCCCCTG

upper sequence: GRMZM2G100639_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT5G46280.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatgctcctactgtttgctctctgcaattttattcaatcaactccatttggtactgtaattgtaatgctgctcaa--cctgtaatggctagGATGACAATGGTAACTTGTTGGTTACCGAGTATGGAATGTGTGAATACAAGGATCACCAGACATTGTCCATGCAAGAAGTGCCTGAAAATTCTGCACCTG
|||    | |  | |||| | ||      || ||| |          |     | |    |  || ||  | |  |    | |  ||   ||||||| || || ||||| ||||| || ||||||||  ||||  ||||||| ||||||||||| ||||| || |||||||||||||||||| |||| ||||
gtaattacatgttttttgttttcgttttgttcatttacctgtactgctggaagatttgcctcttactgaagattgagtttttttttgttcagGATGATAAGGGAAACTTATTGGTGACTGAGTATGGGCTGTGCAAATACAAAGATCACCAGACCTTGTCAATTCAAGAAGTGCCTGAAAATGCTGCTCCTG

upper sequence: GRMZM2G100639_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv10s0003g03080.t01 (Vitis vinifera), 3'ss of exon 4
gtatgctcctactgtttgctctctgcaattttattcaatcaactccatttggtactgtaattgtaatgctgctcaacctgtaatggct-agGATGACAATGGTAACTTGTTGGTTACCGAGTATGGAATGTGTGAATACAAGGATCACCAGACATTGTCCATGCAAGAAGTGCCTGAAAATTCTGCACCTG
   |  |   |     ||   | | | | |  |||   |    |  || |   |       |    |        |     | ||  | ||||||| ||||| ||||| ||||| || ||||||||  ||||  ||||||| || || || || || || ||||||||||||||||| |||||||| || |
--gtaatgtcatgtcatgtcattttctactcaattgttttttatatatataacataagggatagcctttcaagagaaacacactgtttcagGATGAAAATGGCAACTTATTGGTGACTGAGTATGGGTTGTGCAAATACAAAGACCATCAAACCTTATCAATGCAAGAAGTGCCTGAGAATTCTGCTCCAG

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|211158410|gb|FL068715.1|FL068715
EST:     ACATCACATCTTTTGTAGGCTTGCCTACTGGCTCGGTTTATCCAACAAGG                         GATGACAATGGTAACTTGTTGGTTACCGAGTATGGAATGTGTGAATACAAG
genomic: ACATCACATCTTTTGTAGGCTTGCCTACTGGCTCGGTTTATCCAACAAGGgtatgctcct ... taatggctagGATGACAATGGTAACTTGTTGGTTACCGAGTATGGAATGTGTGAATACAAG
EST: gi|211498655|gb|FL137520.1|FL137520
EST:     ACATCACATCTTTTGTAGGCTTGCCTACTGGCTCGGTTTATCCAACAAGG                         GATGACAATGGTAACTTGTTGGTTACCGAGTATGGAATGTGTGAATACAAG
genomic: ACATCACATCTTTTGTAGGCTTGCCTACTGGCTCGGTTTATCCAACAAGGgtatgctcct ... taatggctagGATGACAATGGTAACTTGTTGGTTACCGAGTATGGAATGTGTGAATACAAG
EST: gi|211158409|gb|FL068714.1|FL068714
EST:     ACATCACATCTTTTGTAGGCTTGCCTACTGGCTCGGTTTATCCAACAAGG                         GATGACAATGGTAACTTGTTGGTTACCGAGTATGGAATGTGTGAATAC
genomic: ACATCACATCTTTTGTAGGCTTGCCTACTGGCTCGGTTTATCCAACAAGGgtatgctcct ... taatggctagGATGACAATGGTAACTTGTTGGTTACCGAGTATGGAATGTGTGAATAC
EST: gi|211158412|gb|FL068717.1|FL068717
EST:     ACATCACATCTTTTGTAGGCTTGCCTACTGGCTCGGTTTATCCAACAAGG                         GATGACAATGGTAACTTGTTGGTTACCGAGTATGGAATGTGTGAATACAAG
genomic: ACATCACATCTTTTGTAGGCTTGCCTACTGGCTCGGTTTATCCAACAAGGgtatgctcct ... taatggctagGATGACAATGGTAACTTGTTGGTTACCGAGTATGGAATGTGTGAATACAAG
EST: gi|30306471|gb|CD001144.1|CD001144
EST:     ACATCACATCTTTTGTAGGCTTGCCTACTGGCTCGGTTTATCCAACAAGG                         GATGACAATGGT
genomic: ACATCACATCTTTTGTAGGCTTGCCTACTGGCTCGGTTTATCCAACAAGGgtatgctcct ... taatggctagGATGACAATGGT
EST: gi|211158408|gb|FL068713.1|FL068713
EST:     ACATCACATCTTTTGTAGGCTTGCCTACTGGGTCGGTTTATCCAACAANG                         GATGACAATGGGAACTTGTTGGTTACCGAGTATGGAATGTGTGAATACAAG
genomic: ACATCACATCTTTTGTAGGCTTGCCTACTGGCTCGGTTTATCCAACAAGGgtatgctcct ... taatggctagGATGACAATGGTAACTTGTTGGTTACCGAGTATGGAATGTGTGAATACAAG
EST: gi|211158418|gb|FL068723.1|FL068723
EST:     ACATCACATCTTTTGTAGGCTTGCCTACTGGCTCGGTTTATCCAACAAGG                         GATGACAATGGTAACTTGTTGGNTACCGAGTATGGAATGTGTGAATACAAG
genomic: ACATCACATCTTTTGTAGGCTTGCCTACTGGCTCGGTTTATCCAACAAGGgtatgctcct ... taatggctagGATGACAATGGTAACTTGTTGGTTACCGAGTATGGAATGTGTGAATACAAG
EST: gi|211160000|gb|FL068727.1|FL068727
EST:     ACATCACATCTTTTGTAGGCTTGCCTACTGGCTCGGTTTATCCAACAAGG                         GATGACAATGGTAACTTGTTG
genomic: ACATCACATCTTTTGTAGGCTTGCCTACTGGCTCGGTTTATCCAACAAGGgtatgctcct ... taatggctagGATGACAATGGTAACTTGTTG
EST: gi|74233767|gb|DT641681.1|DT641681
EST:     ACATCACATCTTTTGTAGGCTTGCCTACTGGCTCGGTTTATCCAACAAGG                         GATGACAATGGTAACTTGTTGGTTACCGAGTATGGAATGTGTGAATACAAG
genomic: ACATCACATCTTTTGTAGGCTTGCCTACTGGCTCGGTTTATCCAACAAGGgtatgctcct ... taatggctagGATGACAATGGTAACTTGTTGGTTACCGAGTATGGAATGTGTGAATACAAG
EST: gi|211159998|gb|FL068725.1|FL068725
EST:     ACATCACATCTTTTGTAGGCTTGCCTACTGGCTCGGTTTATCCAACAAGG                         GATGACAATGGTAACTTGTTGGTTACCGAGTATGGAATGTGTGAATACCAG
genomic: ACATCACATCTTTTGTAGGCTTGCCTACTGGCTCGGTTTATCCAACAAGGgtatgctcct ... taatggctagGATGACAATGGTAACTTGTTGGTTACCGAGTATGGAATGTGTGAATACAAG

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: 120

TGTCCACTTCTGCCCTGTGACTGGGGACTTTCTCTCGCGTGAATACAGGGACATCACATCTTTTGTAGGCTTGCCTACTGGCTCGGTTTATCCAACAAGGgtatgctcct ... taatggctagGATGACAATGGTAACTTGTTGGTTACCGAGTATGGAATGTGTGAATACAAGGATCACCAGACATTGTCCATGCAAGAAGTGCCTGAAAATTCTGCACCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 27

TGTCCACTTCTGCCCTGTGACTGGGGACTTTCTCTCGCGTGAATACAGGGACATCACATCTTTTGTAGGCTTGCCTACTGGCTCGGTTTATCCAACAAGGgtatgctcct ... taatggctagGATGACAATGGTAACTTGTTGGTTACCGAGTATGGAATGTGTGAATACAAGGATCACCAGACATTGTCCATGCAAGAAGTGCCTGAAAATTCTGCACCTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 24

TGTCCACTTCTGCCCTGTGACTGGGGACTTTCTCTCGCGTGAATACAGGGACATCACATCTTTTGTAGGCTTGCCTACTGGCTCGGTTTATCCAACAAGGgtatgctcct ... taatggctagGATGACAATGGTAACTTGTTGGTTACCGAGTATGGAATGTGTGAATACAAGGATCACCAGACATTGTCCATGCAAGAAGTGCCTGAAAATTCTGCACCTG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 17

TGTCCACTTCTGCCCTGTGACTGGGGACTTTCTCTCGCGTGAATACAGGGACATCACATCTTTTGTAGGCTTGCCTACTGGCTCGGTTTATCCAACAAGGgtatgctcct ... taatggctagGATGACAATGGTAACTTGTTGGTTACCGAGTATGGAATGTGTGAATACAAGGATCACCAGACATTGTCCATGCAAGAAGTGCCTGAAAATTCTGCACCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatcaactccatttggtactgtaattgtaatgctgctcaacctgtaatggctagGATGACAATGGTAACTTGTTGGTTACCGAGTATGGAATGTGTGAATACAAGGATCACCAGACATTGTCCATGCAAGAAGTGCCTGAAAATTCTGCACCTG
                      taattgtaat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctcctactgtttgctctctgcaattttattcaatcaactccatttggtactgtaattgtaatgctgctcaacctgtaatggctagGATGACAATGGTAACTTGTTGGTTACCGAGTATGGAATGTGTGAATACAAGGATCACCAGACATTGTCCATGCAAGAAGTGCCTGAAAATTCTGCACCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT