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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCGAGAAAAAATATTTCTTCTGTTAGATGCAACACAAACATCCCTTGGTGGAGCTAAAGCAAGGTTCCCTCAGTACTATGAGGCATACTATGAGTTGGTGgtaggtatcatatttgcagctgagaattttccttgattccctttgtttattcccatgtatttgtgttgagaattttggtagcgctatgtttaactgttgg...

Basic information

species Zea mays
transcript GRMZM5G834205_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G834205_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os08g01740.2 (Oryza sativa), 5'ss of exon 5
TCGAGAAAAAATATTTCTTCTGTTAGATGCAACACAAACATCCCTTGGTGGAGCTAAAGCAAGGTTCCCTCAGTACTATGAGGCATACTATGAGTTGGTGgtaggtatcatatttgcagctgagaattttccttgattccct-ttgtttattcccatgtatttgtgttgagaattttggtagcgctatgtttaactgttgg---
||| ||||||||||||||| || | ||||| || ||||||||||||||||||| |||||  |  |||||||||||||||| |||||| ||||||||||||||| |||||||||||  |  |   |  ||   |  || |  | |||   |||   |      |  ||   |||| |   |||  ||||| ||     ||     
TCGTGAAAAAATATTTCTTTTGCTGGATGCGACCCAAACATCCCTTGGTGGAGTTAAAGGGAAATTCCCTCAGTACTATGGGGCATATTATGAGTTGGTGgtatgtatcatattttaatattttatcttcattaaatgctgtgttgaaaatttggacagcactaagt---gaatctgtatagt-ctatggtttttctttaatat

upper sequence: GRMZM5G834205_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA05G33150.1 (Glycine max), 5'ss of exon 6
TCGAGAAAAAATATTTCTTCTGTTAGATGCAACACAAACATCCCTTGGTGGAGCTAAAGCAAGGTTCCCTCAGTACTATGAGGCATACTATGAGTTGGTGgtaggtatcatatttgcagctgagaattttccttgattccctttgtttattcccatgtatttgtgttgagaattttggtagcgctatgtttaactgttgg---
  | ||    |||||||| || |||||||| |||||||||||||||||||| |||   | || ||| || ||||| ||| | ||||| ||||| ||||||||||||| || || ||      | ||     |  |||| ||||   | ||||  || ||  |   ||||  | |  |     ||||   |    | | ||   
AAGGGAGCGGATATTTCTCCTATTAGATGCCACACAAACATCCCTTGGTGGTGCTTCTGGAAAGTTTCCACAGTATTATAATGCATATTATGATTTGGTGgtaggta-cagatatgtgaagtacaaccg--cgagatttcctta--tgattctgatatagattatttgattaataagtggaagctagactattgtttcggcag

upper sequence: GRMZM5G834205_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA06G16740.1 (Glycine max), 5'ss of exon 6
TCGAGAAAAAATATTTCTTCTGTTAGATGCAACACAAACATCCCTTGGTGGAGCTAAAGCAAGGTTCCCTCAGTACTATGAGGCATACTATGAGTTGGTGgtaggtatcatatttgcagctgagaattttccttgattccctttgtttattcccatgtatttgtgttg---agaattttggtagcgctatgtttaactgttgg---
  | ||    |||||||| ||  ||||||| |||||||||||||||||||| ||    | || ||| || ||||| ||| | ||||| ||||| ||||||||||||| || |||||   |  | |||| |  ||   ||   | | ||  |   ||| ||  ||| ||   ||  | |||     || | |    |  |||     
GAGGGAGCGGATATTTCTCCTACTAGATGCCACACAAACATCCCTTGGTGGTGCATCTGGAAAGTTTCCACAGTATTATAATGCATATTATGATTTGGTGgtaggta-cacatttgtgac--acaattatggtttgatc---tggattcatttaatgaataggtggtggctaggctgttgtctaggcaaagaaagaaagtttattt

upper sequence: GRMZM5G834205_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA05G33150.2 (Glycine max), 5'ss of exon 4
TCGAGAAAAAATATTTCTTCTGTTAGATGCAACACAAACATCCCTTGGTGGAGCTAAAGCAAGGTTCCCTCAGTACTATGAGGCATACTATGAGTTGGTGgtaggtatcatatttgcagctgagaattttccttgattccctttgtttattcccatgtatttgtgttgagaattttggtagcgctatgtttaactgttgg-----
  | ||    |||||||| || |||||||| |||||||||||||||||||| |||   | || ||| || ||||| ||| | ||||| ||||| ||||||||||||| || || ||      | ||     |  |||| ||||   | ||||  || ||  |   ||||  | |  |     ||||   |    | | ||     
AAGGGAGCGGATATTTCTCCTATTAGATGCCACACAAACATCCCTTGGTGGTGCTTCTGGAAAGTTTCCACAGTATTATAATGCATATTATGATTTGGTGgtaggta-cagatatgtgaagtacaaccg--cgagatttcctta--tgattctgatatagattatttgattaataagtggaagctagactattgtttcggcagag

upper sequence: GRMZM5G834205_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv07s0031g03190.t01 (Vitis vinifera), 5'ss of exon 4
TCGAGAAAAAATATTTCTTCTGTTAGATGCAACACAAACATCCCTTGGTGGAGCTAAAGCAAGGTTCCCTCAGTACTATGAGGCATACTATGAGTTGGTGgtaggtatcatatttgcagctgagaattttccttgattccctttgtttattcccatgt-atttgtgttgagaattttggtagcgctatgtttaactgttgg---
 ||||| || ||||||||||| |||||||| ||||| ||||| ||||||||||||   |||| ||||||||| |||||    |||||||||||  | |||||| ||||   | | ||| ||     | ||  |    || |||||| |       ||| | ||   |  | | | ||| |   |     | ||     |     
ACGAGAGAAGATATTTCTTCTTTTAGATGCCACACAGACATCACTTGGTGGAGCTTCTGCAAAGTTCCCTCAATACTACAGTGCATACTATGATCTAGTGgtaagtat-gcactggcatctt---gtctttgtatgctctctttgtatgagatgctgttagtttcttcaaaagtcttgcttctgaaggatctattctctcattt

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|71421501|gb|DR805467.1|DR805467
EST:     GAGCTAAAGCAAGGTTCCCTCAGTACTATGAGGCATACTATGAGTTGGTG                         TCTGCTGGTGTGCAATTTTCAAATCGGCCAAATGTTCTTGTCACACGAGCA
genomic: GAGCTAAAGCAAGGTTCCCTCAGTACTATGAGGCATACTATGAGTTGGTGgtaggtatca ... gcctccatagTCTGCTGGTGTGCAATTTTCAAATCGGCCAAATGTTCTTGTCACACGAGCA
EST: gi|78107223|gb|DV525641.1|DV525641
EST:     GAGCTAAAGCAAGGTTCCCTCAGTACTATGAGGCATACTATGAGTTGGTG                         TCTGCTGGTGTGCAATTTTTCAA-TCGGCCAAATGTTCTTGTCACACGAGC
genomic: GAGCTAAAGCAAGGTTCCCTCAGTACTATGAGGCATACTATGAGTTGGTGgtaggtatca ... gcctccatagTCTGCTGGTGTGCAATTTT-CAAATCGGCCAAATGTTCTTGTCACACGAGC
EST: gi|32837204|gb|CD976882.1|CD976882
EST:     ACTATGAGGCATACTATGAGTTGGTG                         TCTGCTGGTGTGCAATTTTCAAATCGGCCAAATGTTCTTGTCACACGAGCA
genomic: ACTATGAGGCATACTATGAGTTGGTGgtaggtatca ... gcctccatagTCTGCTGGTGTGCAATTTTCAAATCGGCCAAATGTTCTTGTCACACGAGCA
EST: gi|149059924|gb|EE157051.2|EE157051
EST:     GAGCTAAAGCAAGGTTCCCTCAGTACTATGAGGCATACTATGAGTTGGTG                         TCTGCTGGTGTGCAATTTTCAAATCGGCCAAATGTTCTTGTCACACGAGCA
genomic: GAGCTAAAGCAAGGTTCCCTCAGTACTATGAGGCATACTATGAGTTGGTGgtaggtatca ... gcctccatagTCTGCTGGTGTGCAATTTTCAAATCGGCCAAATGTTCTTGTCACACGAGCA
EST: gi|93015305|gb|EB640825.1|EB640825
EST:     GAGCTAAAGCAAGGTTCCCTCAATACTATGAGGCATACTATGAGTTGGCG                         TCTGCTGGTGTGCAATTTTCAAATCGGCCAAATGTTCTTGTC
genomic: GAGCTAAAGCAAGGTTCCCTCAGTACTATGAGGCATACTATGAGTTGGTGgtaggtatca ... gcctccatagTCTGCTGGTGTGCAATTTTCAAATCGGCCAAATGTTCTTGTC
EST: gi|149088092|gb|EE287276.2|EE287276
EST:     GAGCTAAAGCAAGGTTCCCTCAGTACTATGAGGCATACTATGAGTTGGTG                         TCTGCTGGTGTGCAATTTTCAAATCGGCCAAATGTTCTTGTCACACGAGCA
genomic: GAGCTAAAGCAAGGTTCCCTCAGTACTATGAGGCATACTATGAGTTGGTGgtaggtatca ... gcctccatagTCTGCTGGTGTGCAATTTTCAAATCGGCCAAATGTTCTTGTCACACGAGCA
EST: gi|9953455|gb|BE640038.1|BE640038
EST:     GAGCTAAAGCAAGGTTCCCTCAGTACTATGAGGCATACTATGAGTTGGTG                         TCTGCTGGTGTGCAATTTTCAAATCGGCCAAATGTTCTTGTCACACGAGCA
genomic: GAGCTAAAGCAAGGTTCCCTCAGTACTATGAGGCATACTATGAGTTGGTGgtaggtatca ... gcctccatagTCTGCTGGTGTGCAATTTTCAAATCGGCCAAATGTTCTTGTCACACGAGCA
EST: gi|71421504|gb|DR805468.1|DR805468
EST:     GAGCTAAAGCAAGGTTCCCTCAGTACTATGAGGCATACTATGAGTTGGTG                         TCTGCTGGTGTGCAATTTTCAAATCGGCCAAATGTTCTTGTCACACGAGCA
genomic: GAGCTAAAGCAAGGTTCCCTCAGTACTATGAGGCATACTATGAGTTGGTGgtaggtatca ... gcctccatagTCTGCTGGTGTGCAATTTTCAAATCGGCCAAATGTTCTTGTCACACGAGCA
EST: gi|71326005|gb|DR799685.1|DR799685
EST:     GAGCTAAAGCAAGGTTCCCTCAGTACTATGAGGCATACTATGAGTTGGTG                         TCTGCTGGTGTGCAATTTTCAAATCGGCCAAATGTTCTTGTCACACGAGCA
genomic: GAGCTAAAGCAAGGTTCCCTCAGTACTATGAGGCATACTATGAGTTGGTGgtaggtatca ... gcctccatagTCTGCTGGTGTGCAATTTTCAAATCGGCCAAATGTTCTTGTCACACGAGCA
EST: gi|78107222|gb|DV525640.1|DV525640
EST:     GAGCTAAAGCAAGGTTCCCTCAGTACTATGAGGCATACTATGAGTTGGTG                         TCTGCTGGTGTGCAATTTTCAAATCGGCCAAATGTTCTTGTCACACGAGCA
genomic: GAGCTAAAGCAAGGTTCCCTCAGTACTATGAGGCATACTATGAGTTGGTGgtaggtatca ... gcctccatagTCTGCTGGTGTGCAATTTTCAAATCGGCCAAATGTTCTTGTCACACGAGCA
EST: gi|50325446|gb|CO520572.1|CO520572
EST:     CTAAAGCAAGGTTCCCTCAGTACTATGAGGCATACTATGAGTTGGTG                         TCTGCTGGTGTGCAATTTTCAAATCGGCCAAATGTTCTTGTCACACGAGCA
genomic: CTAAAGCAAGGTTCCCTCAGTACTATGAGGCATACTATGAGTTGGTGgtaggtatca ... gcctccatagTCTGCTGGTGTGCAATTTTCAAATCGGCCAAATGTTCTTGTCACACGAGCA
EST: gi|44682243|gb|CK787291.1|CK787291
EST:     GAGCTAAAGCAAGGTTCCCTCAGTACTATGAGGCATACTATGAGCTGGTG                         TCTGCTGGTGTGCAATTTTCAAATCGGCCAAATGTTCTTGTCACACGAGCA
genomic: GAGCTAAAGCAAGGTTCCCTCAGTACTATGAGGCATACTATGAGTTGGTGgtaggtatca ... gcctccatagTCTGCTGGTGTGCAATTTTCAAATCGGCCAAATGTTCTTGTCACACGAGCA
EST: gi|148952813|gb|EC898805.2|EC898805
EST:     AGCTAAAAGCAAT-TTCCCTCAGTACTATGAGGCATACTATGAGTTGGTG                         TCTGCTGGTGTGCAATTTTCAA
genomic: AGCTAAA-GCAAGGTTCCCTCAGTACTATGAGGCATACTATGAGTTGGTGgtaggtatca ... gcctccatagTCTGCTGGTGTGCAATTTTCAA
EST: gi|74245587|gb|DT653501.1|DT653501
EST:     GAGCTAAAGCAAGGTTCCCTCAGTACTATGAGGCATACTATGAGTTGGTG                         TCTGCTGGTGTGCAATTTTCAAATCGGCCAAATGTTCTTGTCACACGAGCA
genomic: GAGCTAAAGCAAGGTTCCCTCAGTACTATGAGGCATACTATGAGTTGGTGgtaggtatca ... gcctccatagTCTGCTGGTGTGCAATTTTCAAATCGGCCAAATGTTCTTGTCACACGAGCA
EST: gi|149105965|gb|EE291598.2|EE291598
EST:     GAGCTAAAGCAAGGTTCCCTCAGTACTATGAGGCATACTATGAGTTGGTG                         TCTGCTGGTGTGCAATTTTCAAATCGGCCAAATGTTCTTGTCACACGAGCA
genomic: GAGCTAAAGCAAGGTTCCCTCAGTACTATGAGGCATACTATGAGTTGGTGgtaggtatca ... gcctccatagTCTGCTGGTGTGCAATTTTCAAATCGGCCAAATGTTCTTGTCACACGAGCA
EST: gi|71428013|gb|DR809063.1|DR809063
EST:     GAGCTAAAGCAAGGTTCCCTCAGTACTATGAGGCATACTATGAGTTGGTG                         TCTGCTGGTGTGCAATTTTCAAATCGGCCAAATGTTCTTGTCACACGAGCA
genomic: GAGCTAAAGCAAGGTTCCCTCAGTACTATGAGGCATACTATGAGTTGGTGgtaggtatca ... gcctccatagTCTGCTGGTGTGCAATTTTCAAATCGGCCAAATGTTCTTGTCACACGAGCA
EST: gi|211276223|gb|FL230638.1|FL230638
EST:     GAGCTAAAGCAAGGTTCCCTCAGTACTATGAGGCATACTATGAGTTGGTG                         TCTGCTGGTGTGCAATTTTCAAATCGGCCAAATGTTCTTGTCACACGAGCA
genomic: GAGCTAAAGCAAGGTTCCCTCAGTACTATGAGGCATACTATGAGTTGGTGgtaggtatca ... gcctccatagTCTGCTGGTGTGCAATTTTCAAATCGGCCAAATGTTCTTGTCACACGAGCA
EST: gi|71326004|gb|DR799684.1|DR799684
EST:     GAGCTAAAGCAAGGTTCCCTCAGTACTATGAGGCATACTATGAGTTGGTG                         TCTGCTGGTGTGCAATTTTCAAATCGGCCAAATGTTCTTGTCACACGAGCA
genomic: GAGCTAAAGCAAGGTTCCCTCAGTACTATGAGGCATACTATGAGTTGGTGgtaggtatca ... gcctccatagTCTGCTGGTGTGCAATTTTCAAATCGGCCAAATGTTCTTGTCACACGAGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCGAGAAAAAATATTTCTTCTGTTAGATGCAACACAAACATCCCTTGGTGGAGCTAAAGCAAGGTTCCCTCAGTACTATGAGGCATACTATGAGTTGGTGgtaggtatcatatttgcagctgagaattttccttgattccctttgtttattcccatgtatttgtgttgagaattttggtagcgctatgtttaactgttgg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG