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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctctgcgcgtgtacagcatccaaaatgtgactcttgtatagttgctcaactaggtgttttgattgtactgtttatttacatcattttgctttgtatccagGAATCAACCTCTGCGCGTGTACAGCATGGTGAAATATGCTGCAATAGCACGAGGCGATGCTGAAATCTTCATGAAATTTGCAAGAGCTGGATACAAAGAG

Basic information

species Zea mays
transcript GRMZM2G108364_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G108364_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g56170.1 (Oryza sativa), 3'ss of exon 2
ctctgcgcgtgtacagcatccaaaatgtgactcttgta-tagttgctcaactaggtgtt--ttgattgtactgtt-tatttacatcattttgctttgtatccagGAATCAACCTCTGCGCGTGTACAGCATGGTGAAATATGCTGCAATAGCACGAGGCGATGCTGAAATCTTCATGAAATTTGCAAGAGCTGGATACAAAGAG
  || |   || ||||    |    |    || |||||  |  |  |   | || | |   || || |||||||| |||||| ||  |||||||| |  |||||||| ||||| ||||| ||||||||||||||||||||||| |||||||||||||| ||||  ||||| ||||||||||| || |||||||||||||| |||
--cttcatttg-acagttgtccgtttccatctattgtagcatgtaatttgcaagttttggatttatcgtactgttatatttatat-gttttgcttggattccagGAAGCAACCCCTGCGTGTGTACAGCATGGTGAAATATGCCGCAATAGCACGAGGGGATGTAGAAATATTCATGAAATTCGCTAGAGCTGGATACAAGGAG

upper sequence: GRMZM2G108364_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA13G25470.1 (Glycine max), 3'ss of exon 1
ctctgcgcgtgtacagcatccaaaatgtgactcttgtatagttgctcaa--ctaggtgttttgattgtactgtttatt---tacatcattttgc-tttgtatccagGAATCAACCTCTGCGCGTGTACAGCATGGTGAAATATGCTGCAATAGCACGAGGCGATGCTGAAATCTTCATGAAATTTGCAAGAGCTGGATACAAAGAG
           |  |  ||  ||||||| |||     |  ||  |  ||  | |  |   ||  | | |  ||||||    || || |||   | ||| ||| ||| ||||| ||  |  | || |||| |||| |||||||||||||||||||  | || ||||||||  | |||||||| |||||||| ||||| ||||| |||
------aaagattgaatatttaaaatgtcacttggtaaaggtcaccaaagacaacataaatttctagcatagtttataaggtatattattcgtcatttatatgcagTAATCAGCCAGTAAGAGTATACAACATGATGAAATATGCTGCAATAGCTTGTGGGGATGCTGAGGTTTTCATGAAGTTTGCAAGGGCTGGTTACAAGGAG

upper sequence: GRMZM2G108364_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA13G31850.1 (Glycine max), 3'ss of exon 2
-ctctgcgcgtgtacagcatccaaaatgtgactcttgtatagttgctcaactaggtgttttgattgta--ctgtttatttacatcattttgctt-tgtatccagGAATCAACCTCTGCGCGTGTACAGCATGGTGAAATATGCTGCAATAGCACGAGGCGATGCTGAAATCTTCATGAAATTTGCAAGAGCTGGATACAAAGAG
  |       | |  ||  |   |||   ||| |           |  || |   | | ||  ||  |   |  | |  ||  || ||||  |  ||||| |||||| || ||  || | |||||||||||||||||||| || |||||||| || || ||||||||  | |||||||| |||||||| || || ||||| |||
attaaaaatatctttagtttaggaaa-aagacacaaacgcg---acataatttattatcttagtttcagcttaataagatatctctttttcatcatgtatgcagGAAACAGCCATTGAGGGTGTACAGCATGGTGAAATACGCAGCAATAGCTCGTGGGGATGCTGAGGTTTTCATGAAGTTTGCAAGGGCCGGTTACAAGGAG

upper sequence: GRMZM2G108364_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA15G07450.1 (Glycine max), 3'ss of exon 2
ctctgcgcgtgtacagcatccaaaatgtgactcttgtatagt-tgctcaactaggt--gttttgattgtactgtttatttacatcattttgctttgtatccagGAATCAACCTCTGCGCGTGTACAGCATGGTGAAATATGCTGCAATAGCACGAGGCGATGCTGAAATCTTCATGAAATTTGCAAGAGCTGGATACAAAGAG
 |   |   | |  ||  |    ||    || |   |  |   |  |  | ||| |  |||||   | ||     ||| |   |  |||      || | |||||| |||||  || | || |||||||||||||||||||| |||||||| || || ||||||||  | |||||||| |||||||| ||||| ||||| |||
ttaaacatatctttagtttagggaaaaaaacacaaatgcaacataatttattagcttagttttagctttataagatatct---ttttttcatcacgtgtgcagGAAACAACCATTGAGGGTATACAGCATGGTGAAATATGCAGCAATAGCTCGTGGGGATGCTGAGGTTTTCATGAAGTTTGCAAGGGCTGGTTACAAGGAG

upper sequence: GRMZM2G108364_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA12G22680.1 (Glycine max), 3'ss of exon 2
ctctgcgcgtgtacagcatccaaaat-gtgactcttgtatagttgctcaactaggtgttttgattgtactgt-ttatttacatcattttgctttgtatccagGAATCAACCTCTGCGCGTGTACAGCATGGTGAAATATGCTGCAATAGCACGAGGCGATGCTGAAATCTTCATGAAATTTGCAAGAGCTGGATACAAAGAG
   |      | |  | | |  |  |  ||||| || |||  ||  |     |      ||  | ||| ||  ||  |     | ||     |  | | ||| || || ||  |||||||| |||||||||| ||||| || |||||||| ||||| || || || || ||||||||||||||||     || ||||| |||
--ttctttcagaattgtacctgagcttatgacttttttatttttcttttttgaaaacgatttctggtattgaattgctcttccctttcaaaatcttttacagAAAACAGCCCTTGCGCGTGCACAGCATGGTAAAATACGCAGCAATAGCCCGAGGAGACGCGGAGATATTCATGAAATTTGCAAAGTGCGGCTACAAGGAG

upper sequence: GRMZM2G108364_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA07G31080.1 (Glycine max), 3'ss of exon 2
ctctgcgcgtgtacagcatccaaaatgtgactcttgtatagttgctcaactaggtgt---tttgattgtactgttta-----tttacatcattttgctttgtatccagGAATCAACCTCTGCGCGTGTACAGCATGGTGAAATATGCTGCAATAGCACGAGGCGATGCTGAAATCTTCATGAAATTTGCAAGAGCTGGATACAAAGAG
         | || || |||    || | |||     |  || ||  ||  | |  |   ||   | | |  |||||     |    || |||   |  | ||| ||| ||||| || ||| | || |||| || | |||||||| | ||||||||| | || ||||||||  | ||||| ||||||||||||||||| ||||| |||
-------tatttaaagtatcactcat-tcacttggtaaaggtcgccaaagaaagcataaattctctagcatagtttagaaggtaactattattcatcgctatatgcagTAATCAGCCACTGAGAGTATACAACACGATGAAATATACGGCAATAGCATGTGGGGATGCTGAGGTTTTCATAAAATTTGCAAGAGCTGGTTACAAGGAG

upper sequence: GRMZM2G108364_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv00s0301g00050.t01 (Vitis vinifera), 3'ss of exon 2
-ctctgcgcgtgtacagcatccaaaatgtgactctt-gtatagttgctcaactaggtgttttgattgtactgtttatttacatcattttgctttgtatccagGAATCAACCTCTGCGCGTGTACAGCATGGTGAAATATGCTGCAATAGCACGAGGCGATGCTGAAATCTTCATGAAATTTGCAAGAGCTGGATACAAAGAG
  |      |   |  |||   | ||  | | |    | | |  ||   |||         ||  |  | ||  || || | |  ||  | ||    | |||||| |||||  | || || |||||||||||||| ||||| || ||||| || || ||||| || || || ||||| |||||||||||||| ||||| || 
aatgataatgaaaatggcagatagaagataattaaaagaagaaatggaaaacagaaacacatgtgttcattgagtagtttctt--ttccgtttcaactgcagGAAGCAACCGTTACGTGTATACAGCATGGTGAAGTATGCAGCCATAGCCCGTGGTGATGCAGAGATTTTTATGAAGTTTGCAAGAGCTGGCTACAAGGAA

upper sequence: GRMZM2G108364_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv19s0014g03380.t01 (Vitis vinifera), 3'ss of exon 2
ctctgcgcgtgtacagcatccaaaatgtgactcttgtatagttgctcaactaggtgttttgattgtactgtttatttacatcattttgctttgtatc-----cagGAATCAACCTCTGCGCGTGTACAGCATGGTGAAATATGCTGCAATAGCACGAGGCGATGCTGAAATCTTCATGAAATTTGCAAGAGCTGGATACAAAGAG
   |   |   ||    |       |  |||  ||    | |||   |||| ||  | |   |   | || || |    |  || || || | |  |     ||| || || ||| ||||||| || ||||||||||| ||||| || ||||| || || |||||||| || || ||||| |||||||||||||||||||| |||
--ttttaccaatatgttaggatggcttcgaccatta---aattgtctaacttgggctatgcctaaaattgattctcataaatatatttctatattccaatggcagAAAGCAGCCTTTGCGCGTCTATAGCATGGTGAAGTATGCAGCCATAGCCCGGGGAGATGCTGAGATTTTTATGAAGTTTGCAAGAGCTGGATACAAGGAG

upper sequence: GRMZM2G108364_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S158_188V6.1 (Physcomitrella patens), 3'ss of exon 4
ctctgcgcgtgtacagcatccaaaatgtgactcttgtatagttgctcaact--aggtgttttgattgtactgtttatttacatcattttgctttgtatccagGAATCAACCTCTGCGCGTGTACAGCATGGTGAAATATGCTGCAATAGCACGAGGCGATGCTGAAATCTTCATGAAATTTGCAAGAGCTGGATACAAAGAG
 | |     |   |   ||   ||     |   |  || || |||   |||  ||   | |   |  |     | | |||    | | | || | || |||||||||| || ||||| || ||||| ||||  ||||| || || || || || || ||||| || ||||||||||| ||||||| ||||||||| || |||
-tata-atttaatccttatgttaatcaacaaattcttaaagctgcaatactgtagacttctaagtcctggatctaagttagtcgactcttctatttaaccagGAATCAGCCGCTGCGAGTCTACAGTATGGCCAAATACGCAGCCATTGCTCGGGGTGATGCAGAGATCTTCATGAAGTTTGCAAAAGCTGGATATAAGGAG

upper sequence: GRMZM2G108364_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S47_263V6.1 (Physcomitrella patens), 3'ss of exon 4
---ctctgcgcgtgtacagcatccaaaatgtgact-cttgtatagttgctcaactaggtgttttgattgtactgtttatttacatcattttgctttgtatccagGAATCAACCTCTGCGCGTGTACAGCATGGTGAAATATGCTGCAATAGCACGAGGCGATGCTGAAATCTTCATGAAATTTGCAAGAGCTGGATACAAAGAG
     || |   |  |     | |||||      | | | |  | ||  |  ||     ||   |  |    | |  | |    || || || |||||  ||||||||||||| ||||| || ||||||||||  ||||| || ||  | || ||||| ||||| |||||||||||||| ||||||| |||||| |||||||||
ttgacctacctattcaatcttttcaaaaaagagttacgtctgcatttcttttac--accgtcaagtctaggatttgaactagtgtctttctgttttgt--ccagGAATCAACCACTGCGAGTCTACAGCATGGCCAAATACGCAGCCGTTGCTCGAGGGGATGCAGAAATCTTCATGAAGTTTGCAAAAGCTGGGTACAAAGAG

upper sequence: GRMZM2G108364_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ19025 (Selaginella moellendorffii), 3'ss of exon 2
ctctgcgcgtgtacagcatccaaaatgtgactcttgtatagttgctcaactaggtgttttgattgtactgtttatttacatcattttgctttgtatccagGAATCAACCTCTGCGCGTGTACAGCATGGTGAAATATGCTGCAATAGCACGAGGCGATGCTGAAATCTTCATGAAATTTGCAAGAGCTGGATACAAAGAG
                                           |  |    | || |||   |   |  |   |     | | |||||  |      |||||| |  ||  | || || ||||| |||| ||| ||||| ||||| || || ||||| || || |||||||||||||| |||||||| || ||||| |||
-------------------------------------------gtacgcgaaagtctttctctgcgagcggcaaaaactaac-ttttgtctccctggcagGAAACGTCCGTTACGGGTCTACAGTATGGCGAAGTATGCAGCAATTGCTCGTGGCGACGCGGAGATCTTCATGAAATTCGCAAGAGCGGGTTACAAGGAG

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|149072983|gb|EE161244.2|EE161244
EST:     CATTCCTTCACAGCAGGACTTGCTCAAAGTGTAGGATTAAG                         GAATCAACCTCTGCGCGTGTACAGCATGGTGAAATATGCTGCAATAGCACG
genomic: CATTCCTTCACAGCAGGACTTGCTCAAAGTGTAGGATTAAGgtcagttctt ... ttgtatccagGAATCAACCTCTGCGCGTGTACAGCATGGTGAAATATGCTGCAATAGCACG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaactaggtgttttgattgtactgtttatttacatcattttgctttgtatccagGAATCAACCTCTGCGCGTGTACAGCATGGTGAAATATGCTGCAATAGCACGAGGCGATGCTGAAATCTTCATGAAATTTGCAAGAGCTGGATACAAAGAG
           ttttgat  putative branch site (score: 4)
                                      ttttgcttt  putative PPT
                         tttatttacatcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctctgcgcgtgtacagcatccaaaatgtgactcttgtatagttgctcaactaggtgttttgattgtactgtttatttacatcattttgctttgtatccagGAATCAACCTCTGCGCGTGTACAGCATGGTGAAATATGCTGCAATAGCACGAGGCGATGCTGAAATCTTCATGAAATTTGCAAGAGCTGGATACAAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA