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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgttggtctgactagttacatttttgtgtaattaattgtgttggtctgactagttacatttttgtgtaattaattgtttttcacttttctgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTCATTGCTCAATGCTTTATA

Basic information

species Zea mays
transcript GRMZM2G059381_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G059381_T03 (Zea mays), 3'ss of exon 5
lower sequence: AT5G27600.1 (Arabidopsis thaliana), 3'ss of exon 18
gtgttggtctgactagttacatttttgtgtaattaattgtgttggtctgactagttacatttttgtgtaattaattgtttttcacttttctgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTCATTGCTCAATGCTTTATA
      || | |  | | | |   || |    ||| || | |   | ||   |   | |  ||    |  ||  |     |||| | | |    |   ||||| |||||||| || ||||| || ||||||||||| ||||| ||||||||||| || ||||| ||| | || || |  ||| || | || || || || 
------gttttataaatcaaaacattctt--gttatttctttc--tttgcggaagaaaaagttgaaatgtttgttaaaacttcaatgtgc---atgacagGAAGAAGAACATATTTAAGTTGGCGCAAGGAGAATATATAGCACCAGAGAAGATCGAAAATGTTTATACCAAATGTAGATTCGTTTCGCAGTGTTTCATT

upper sequence: GRMZM2G059381_T03 (Zea mays), 3'ss of exon 5
lower sequence: Vv14s0128g00720.t01 (Vitis vinifera), 3'ss of exon 18
gtgttggtctgactagttacatttttgtgtaattaattgtgttgg-tctgactagttacatttttgtgtaattaattgtttttcacttttctgggttga-agGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTCATTGCTCAATGCTTTATA
   ||| |   |  ||  || || |   |      |   ||     | | | |  | | ||||| || |  |||       || |           ||| |||||||||||||| |||||| | || || || ||||| ||||| |||||||| ||||||||||| ||||| |||||||| ||  || | ||||| ||||| 
-aattgcttacaaaagaaactttgtgaagagcaggaacatgccaactttaagttatgaaattttagtctc-ttagcgaaaattgatggccaacttatgacagGAAAAAGAACATCTTCAAGCTGGCACAGGGTGAATATATAGCACCAGAGAAAATTGAGAATGTATATGCCAAGTGCAAATTTGTTTCCCAATGTTTTATC

upper sequence: GRMZM2G059381_T03 (Zea mays), 3'ss of exon 5
lower sequence: Vv05s0020g03080.t01 (Vitis vinifera), 3'ss of exon 18
--------------------------------------------------------------------------------------------gtgttggtctgactagttacatttttgtgtaattaattgtgttggtctgactagttacatttttgtgtaattaatt-gtttttcacttttctgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTCATTGCTCAATGCTTTATA
                                                                                             | ||||||     | ||   | ||  | ||||  | | |  |    |   |  |||| | |   | |  |   || || ||  |  ||  |   |   ||||| ||||||||||| ||||| || |||||||| ||||||||||||||||| ||||||||||| |||||||| ||||| ||  |||| || |||||| ||
gtaaagaccatatcatttttgttgacagttcttagacgaattaataatgactcctctctagttttggatgactcaattgactgtatgttcatatcttggtcctgtgattttgttattgatataatcgactataattacatacttcattacctgtgcatttcttagctttgtattaaaagttgttatatgacagGAAGAAGAACATTTTTAAGTTGGCACAAGGAGAGTACATAGCTCCAGAGAAAATTGAGAATGTATATGCTAAATGCAAATTTGTTGCCCAGTGCTTTGTA

upper sequence: GRMZM2G059381_T03 (Zea mays), 3'ss of exon 5
lower sequence: PP1S408_23V6.1 (Physcomitrella patens), 3'ss of exon 20
-gtgttggtctgactagttacatttttgtgtaattaattgtgttggtctgactagttacatttttgtgtaattaattgtttt-tcacttttc-tgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTCATTGCTCAATGCTTTATA
 ||  ||    ||  | ||    ||||   |  | |    ||||      | |||| |  || |  | |   |  |||||   ||| |  ||     ||| ||||| ||||| || || ||||| ||||||||||| ||||| || || |||||||| |||||||||||   |    |    |||||  | || || |  |||
tgtcgtgagtggatcaatttagcttttactttttcaggaatgttcac--aagtagt-atgttctgttcttcgtgtttgttgagtcattcatcacacattgcagGAAGAAGAATATCTTTAAGTTGGCTCAAGGAGAGTACATTGCCCCGGAGAAGATCGAGAATGTCTACCTTCGCAGTCGTTTCATAACACAGTGTTACATA

upper sequence: GRMZM2G059381_T03 (Zea mays), 3'ss of exon 5
lower sequence: PP1S33_126V6.1 (Physcomitrella patens), 3'ss of exon 21
------------------------------------------------------------------------------gtgttggtctgacta-gttacatttttgtgtaattaattgtgttggtctgactagttacatttttg----tgtaattaattgtttttcacttttctgg--gttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTCATTGCTCAATGCTTTATA
                                                                              ||       ||| || |||  | | || |    ||    |  |   ||  |||    | ||||  |    | | || | ||||   |   ||   |||   ||| || || ||||| || |||||||| ||||| ||||| ||||| || || |||||||||||||| |||||        |   ||||||||| || |||||||| 
gtactctggactagcgtcacccttagatgtatgctattgatatttttcatcattcaacgtctggtagtctagatcagtgtacccagttgagtatgttctactcttctaatgttcgaag-atcaatccaactttgaatatttcaggagctttcatgagttgtacgttctttccttggttattgcagAAAGAAGAATATCTTCAAGTTGGCTCAGGGAGAGTACATTGCGCCCGAGAAGATTGAGAACGTCTACCTGCGAAGTCGGTTCATTGCACAGTGCTTTATT

upper sequence: GRMZM2G059381_T03 (Zea mays), 3'ss of exon 5
lower sequence: PP1S12_178V6.2 (Physcomitrella patens), 3'ss of exon 20
--gtgttggtctgactagttacatttttgtgtaattaattgtgttggtctgactagttacatttttgtgtaattaattgtttttcacttttctgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTCATTGCTCAATGCTTTATA
  || ||  |||     |  || | |   |  ||  |||| | | |   || |   |   ||  |  |||  |   |||| |       |    |  || ||||| ||||||||||||||||||||||||||||||||||| || || || |||||||||||  | |||  |    |   ||| ||| | || || ||  ||
aagttttattcttctctgaaac-tgtaactagaaaaaattatctggaagtggcagttcttatgctcatgtt-tgttttgtatcctttaatcactgtctgcagGAAGAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATTGCACCGGAAAAGATTGAGAACATTTATCTTCGCAGTCGGTTTATTTCGCAGTGTTTCGTA

upper sequence: GRMZM2G059381_T03 (Zea mays), 3'ss of exon 5
lower sequence: EFJ37488 (Selaginella moellendorffii), 3'ss of exon 19
gtgttggtctgactagttacatttttgtgtaattaattgtgttggtctgactagttacat-ttttgtgtaatt-aattgtttttcacttttctgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTCATTGCTCAATGCTTTATA
                                                     || || |  ||||||| |||  ||| |  || || |   |   |   ||||||||||||||||| ||| | || || || ||||||||||| ||||||||||||||||||||||||   ||  |||||||| ||||||| || ||  | 
-----------------------------------------------------gtaacgtgctttgtgtcattcgattttgcttgacgtcattttttgccagGAAAAAGAACATTTTTAAGCTTGCACAGGGTGAATACATAGCGCCAGAGAAGATTGAGAATGTCTATCAAAAAAGCAAGTTCGTTGCTCAGTGTTTCGTC

upper sequence: GRMZM2G059381_T03 (Zea mays), 3'ss of exon 5
lower sequence: EFJ33980 (Selaginella moellendorffii), 3'ss of exon 19
gtgttggtctgactagttacatttttgtgtaattaattgtgttggtctgactagttacat-ttttgtgtaatt-aattgtttttcacttttctgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTCATTGCTCAATGCTTTATA
                                                     || || |  ||||||| |||  ||| |  || || |   |   |   ||||||||||||||||| ||| | || || || ||||||||||| ||||||||||||||||||||||||  |||  |||||||| ||||||| || ||  | 
-----------------------------------------------------gtaacgtgctttgtgtcattcgattttgcttgacgtcattttttgccagGAAAAAGAACATTTTTAAGCTTGCACAGGGTGAATACATAGCGCCAGAGAAGATTGAGAATGTCTATCATAAAAGCAAGTTCGTTGCTCAGTGTTTCGTC

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|60395514|gb|DN228384.1|DN228384
EST:     GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAG                         GAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
genomic: GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaagctga ... tgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
EST: gi|9732348|gb|BE511100.1|BE511100
EST:     GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAG                         GAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
genomic: GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaagctga ... tgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgactagttacatttttgtgtaattaattgtttttcacttttctgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTCATTGCTCAATGCTTTATA
                       aattaat  putative branch site (score: 3)
                             ttgtttttcacttttc  CT-rich tract
         ttacatttttgtgtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgttggtctgactagttacatttttgtgtaattaattgtgttggtctgactagttacatttttgtgtaattaattgtttttcacttttctgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTCATTGCTCAATGCTTTATA

-tgttggt
- - - - - - - - -tacattt