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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCGAGAAAAAATATTTCTTCTGTTAGATGCCACGCAAACATCCCTTGGTGGAGCTAAAGCAAAGTTTCCTCAGTACTATGAGGCATACTATGAGCTGGTGgtaggtaccatatttacagttttcttcttttgcttggcttcctttgtttcctcccatgtatttgtattgggaattttggtagcactgtttttaactcttg...

Basic information

species Zea mays
transcript GRMZM2G135568_T04
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G135568_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os08g01740.2 (Oryza sativa), 5'ss of exon 5
TCGAGAAAAAATATTTCTTCTGTTAGATGCCACGCAAACATCCCTTGGTGGAGCTAAAGCAAAGTTTCCTCAGTACTATGAGGCATACTATGAGCTGGTGgtaggtaccatatttacagttttcttcttttgcttggcttcctttgtttcctcccatgtatttgtattgggaattttggtag--cactgtttttaactcttg-
||| ||||||||||||||| || | ||||| || ||||||||||||||||||| |||||  || || ||||||||||||| |||||| |||||| |||||||| ||| |||||||  | | || |   ||   |     | || ||||         |          | |||| |   |||   |  ||||||   |  |  
TCGTGAAAAAATATTTCTTTTGCTGGATGCGACCCAAACATCCCTTGGTGGAGTTAAAGGGAAATTCCCTCAGTACTATGGGGCATATTATGAGTTGGTGgtatgtatcatattt-taatattttatcttcattaaa--tgctgtgttgaaaatttggacagcactaagtgaatctgtatagtctatggtttttctttaatat

upper sequence: GRMZM2G135568_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA05G33150.1 (Glycine max), 5'ss of exon 6
TCGAGAAAAAATATTTCTTCTGTTAGATGCCACGCAAACATCCCTTGGTGGAGCTAAAGCAAAGTTTCCTCAGTACTATGAGGCATACTATGAGCTGGTGgtaggtacc-atatttacagttttcttcttttgcttggcttcctttgtttcctcccatg---tatttgtattgggaattttggtagcactgtttttaactcttg
  | ||    |||||||| || ||||||||||| ||||||||||||||||| |||   | ||||||||| ||||| ||| | ||||| |||||  |||||||||||||  |||| |  |||      |    ||  |  ||||||    | ||   ||    ||||||  |    | |    |    ||| || ||    |   
AAGGGAGCGGATATTTCTCCTATTAGATGCCACACAAACATCCCTTGGTGGTGCTTCTGGAAAGTTTCCACAGTATTATAATGCATATTATGATTTGGTGgtaggtacagatatgtgaagt-----acaaccgcgagatttccttatgattctgatatagattatttgattaataagtggaagctagactattgtttcggcag-

upper sequence: GRMZM2G135568_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA06G16740.1 (Glycine max), 5'ss of exon 6
TCGAGAAAAAATATTTCTTCTGTTAGATGCCACGCAAACATCCCTTGGTGGAGCTAAAGCAAAGTTTCCTCAGTACTATGAGGCATACTATGAGCTGGTGgtaggtac-catattt-acagttttcttcttttgcttggcttcctttgtttcctcccatgtatttgtattgggaattttg-gtagcactgtttttaactcttg
  | ||    |||||||| ||  |||||||||| ||||||||||||||||| ||    | ||||||||| ||||| ||| | ||||| |||||  ||||||||||||| ||| | | |||   || |  |||    ||| ||| |||  |   |     ||   |    ||     |  |   || |      || | |    
GAGGGAGCGGATATTTCTCCTACTAGATGCCACACAAACATCCCTTGGTGGTGCATCTGGAAAGTTTCCACAGTATTATAATGCATATTATGATTTGGTGgtaggtacacatttgtgacacaattatggtttgatctggattcatttaatgaataggtggtggctaggctgttgtctaggcaaagaaagaaagtttattt---

upper sequence: GRMZM2G135568_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA05G33150.2 (Glycine max), 5'ss of exon 4
TCGAGAAAAAATATTTCTTCTGTTAGATGCCACGCAAACATCCCTTGGTGGAGCTAAAGCAAAGTTTCCTCAGTACTATGAGGCATACTATGAGCTGGTGgtaggtacc-atatttacagttttcttcttttgcttggcttcctttgtttcctcccatg---tatttgtattgggaattttggtagcactgtttttaactcttg-
  | ||    |||||||| || ||||||||||| ||||||||||||||||| |||   | ||||||||| ||||| ||| | ||||| |||||  |||||||||||||  |||| |  |||      |    ||  |  ||||||    | ||   ||    ||||||  |    | |    |    ||| || ||    |    
AAGGGAGCGGATATTTCTCCTATTAGATGCCACACAAACATCCCTTGGTGGTGCTTCTGGAAAGTTTCCACAGTATTATAATGCATATTATGATTTGGTGgtaggtacagatatgtgaagt-----acaaccgcgagatttccttatgattctgatatagattatttgattaataagtggaagctagactattgtttcggcagag

upper sequence: GRMZM2G135568_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA08G00750.1 (Glycine max), 5'ss of exon 5
TCGAGAAAAAATATTTCTTCTGTTAGATGCCACGCAAACATCCCTTGGTGGAGCTAAAGCAAAGTTTCCTCAGTACTATGAGGCATACTATGAGCTGGTGgtaggtacc-atatttacagttttcttcttttgcttggcttcctttgtttcctcccatgtatttgtattgggaattttggtagcactgtt-tttaactcttg
  | ||    |||||||| ||  |||||||||| ||||||||||| ||||| |||   | ||||||||| || || ||| | ||||| |||||  |||||||||||||  |||  |  |||      ||     ||  | |  |   | |  |      ||||||  |    | |    |    ||| || ||| |     |
AAGGGAGCGGATATTTCTCCTACTAGATGCCACACAAACATCCCTAGGTGGCGCTTCTGGAAAGTTTCCACAATATTATAATGCATATTATGATTTGGTGgtaggtacagataagtgaagtacaaccctgagattt--ccttatgattctgatatagattatttgattaataagtggcagctagactattgttttagcagag

upper sequence: GRMZM2G135568_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA04G38320.2 (Glycine max), 5'ss of exon 6
TCGAGAAAAAATATTTCTTCTGTTAGATGCCACGCAAACATCCCTTGGTGGAGCTAAAGCAAAGTTTCCTCAGTACTATGAGGCATACTATGAGCTGGTGgtaggtaccatatttacagttttcttcttttgcttggcttcctttgtttcctcccatgtatttgtattgggaattttggtagcactgtttttaactcttg-
  | ||    |||||||| ||  |||||||||| |||||||||||| |||| ||    | ||||||||| ||||| ||| | ||||| |||||  ||||||||||||| | ||||           |  | |       |  |   ||       ||  |||||         |  |||     ||||| |  |  |    
CAGGGAGCGGATATTTCTCCTACTAGATGCCACACAAACATCCCTTCGTGGTGCATCTGGAAAGTTTCCACAGTATTATAATGCATATTATGATTTGGTGgtaggtac-acatttgtgacacaaacccctgggacattcttatggtttgatctggattcatttgatgaataggtggtggctaggctgttgtctaggcaaag

upper sequence: GRMZM2G135568_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv07s0031g03190.t01 (Vitis vinifera), 5'ss of exon 4
TCGAGAAAAAATATTTCTTCTGTTAGATGCCACGCAAACATCCCTTGGTGGAGCTAAAGCAAAGTTTCCTCAGTACTATGAGGCATACTATGAGCTGGTGgtaggtaccatatttacagttttcttcttttgcttggcttcctttgtttcctcccatgt-atttgtattgggaattttggtagcactgtttttaa-ctcttg---
 ||||| || ||||||||||| ||||||||||| || ||||| ||||||||||||   |||||||| ||||| |||||    ||||||||||| || |||||| |||     |  || |   |||| | ||  |  |||  |||||| |       ||| | ||   |    | | ||| |      |  | ||  ||||     
ACGAGAGAAGATATTTCTTCTTTTAGATGCCACACAGACATCACTTGGTGGAGCTTCTGCAAAGTTCCCTCAATACTACAGTGCATACTATGATCTAGTGgtaagta-----tgcactggcatcttgtctttgtatgctctctttgtatgagatgctgttagtttcttcaaaagtcttgcttctgaaggatctattctctcattt

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|149082655|gb|EE171861.2|EE171861
EST:     GAGCTAAAGCAAAGTTTCCTCAGTACTATGAGGCATACTATGAGCTGGTG                         TCTGCTGGTGTGCAATTTTCAAATCGCCCAAATGTTGTTGTCACACGAGCA
genomic: GAGCTAAAGCAAAGTTTCCTCAGTACTATGAGGCATACTATGAGCTGGTGgtaggtacca ... gcctccatagTCTGCTGGTGTGCAATTTTCAAATCGCCCAAATGTTGTTGTCACACGAGCA
EST: gi|71757755|gb|DR955692.1|DR955692
EST:     GAGCTAAAGCAAAGTTTCCTCAGTACTATGAGGCATACTATGAGCTGGTG                         TCTGCTGGTGTGCAATTTTCAAATCGCCCAAATGTTGTTGTCACACGAGCA
genomic: GAGCTAAAGCAAAGTTTCCTCAGTACTATGAGGCATACTATGAGCTGGTGgtaggtacca ... gcctccatagTCTGCTGGTGTGCAATTTTCAAATCGCCCAAATGTTGTTGTCACACGAGCA
EST: gi|149061138|gb|EE157398.2|EE157398
EST:     GAGCTAAAGCAAAGTTTCCTCAGTACTATGAGGCATACTATGAGCTGGTG                         TCTGCTGGTGTGCAATTTTCAAATCGCCCAAATGTTGTTGTCACACGAGCA
genomic: GAGCTAAAGCAAAGTTTCCTCAGTACTATGAGGCATACTATGAGCTGGTGgtaggtacca ... gcctccatagTCTGCTGGTGTGCAATTTTCAAATCGCCCAAATGTTGTTGTCACACGAGCA
EST: gi|89249738|gb|DY621524.1|DY621524
EST:     GAGCTAAAGCAAAGTTTCCTCAGTACTATGAGGCATACTATGAGCTGGTG                         TCTGCTGGTGTGCAATTTTCAAATCGCCCAAATGTTGTTGTCACACGAGCA
genomic: GAGCTAAAGCAAAGTTTCCTCAGTACTATGAGGCATACTATGAGCTGGTGgtaggtacca ... gcctccatagTCTGCTGGTGTGCAATTTTCAAATCGCCCAAATGTTGTTGTCACACGAGCA
EST: gi|149061139|gb|EE157399.2|EE157399
EST:     GAGCTAAAGCAAAGTTTCCTCAGTACTATGAGGCATACTATGAGCTGGTG                         TCTGCTGGTGTGCAATTTTCAAATCGCCCAAATGTTGTTGTCACACGAGCA
genomic: GAGCTAAAGCAAAGTTTCCTCAGTACTATGAGGCATACTATGAGCTGGTGgtaggtacca ... gcctccatagTCTGCTGGTGTGCAATTTTCAAATCGCCCAAATGTTGTTGTCACACGAGCA
EST: gi|149083911|gb|EE173287.2|EE173287
EST:     GAGCTAAAGCAAAGTTTCCTCAGTACTATGAGGCATACTATGAGCTGGTG                         TCTGCTGTTGTGCAATTTTC
genomic: GAGCTAAAGCAAAGTTTCCTCAGTACTATGAGGCATACTATGAGCTGGTGgtaggtacca ... gcctccatagTCTGCTGGTGTGCAATTTTC
EST: gi|149083910|gb|EE173286.2|EE173286
EST:     GAGCTAAAGCAAAGTTTCCTCAGTACTATGAGGCATACTATGAGCTGGTG                         TCTGCTGGTGTGCAATTTTCAAATCGCCCAAATGTTGTTGTCACACGAGCA
genomic: GAGCTAAAGCAAAGTTTCCTCAGTACTATGAGGCATACTATGAGCTGGTGgtaggtacca ... gcctccatagTCTGCTGGTGTGCAATTTTCAAATCGCCCAAATGTTGTTGTCACACGAGCA
EST: gi|88748264|gb|DY532405.1|DY532405
EST:     AAGCAAAGTTTCCTCAGTACTATGAGGCATACTATGAGCTGGTG                         TCTGCTGGTGTGCAA-TTTCAAATCGCCCAAATGTTGTTGTCACACGAGCA
genomic: AAGCAAAGTTTCCTCAGTACTATGAGGCATACTATGAGCTGGTGgtaggtacca ... gcctccatagTCTGCTGGTGTGCAATTTTCAAATCGCCCAAATGTTGTTGTCACACGAGCA
EST: gi|71757754|gb|DR955691.1|DR955691
EST:     GAGCTAAAGCAAAGTTTCCTCAGTACTATGAGGCATACTATGAGCTGGTG                         TCTGCTGGTGTGCAATTTTCAAATCGCCCAAATGTTGTTGTCACACGAGCA
genomic: GAGCTAAAGCAAAGTTTCCTCAGTACTATGAGGCATACTATGAGCTGGTGgtaggtacca ... gcctccatagTCTGCTGGTGTGCAATTTTCAAATCGCCCAAATGTTGTTGTCACACGAGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCGAGAAAAAATATTTCTTCTGTTAGATGCCACGCAAACATCCCTTGGTGGAGCTAAAGCAAAGTTTCCTCAGTACTATGAGGCATACTATGAGCTGGTGgtaggtaccatatttacagttttcttcttttgcttggcttcctttgtttcctcccatgtatttgtattgggaattttggtagcactgtttttaactcttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG