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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttggatgtaagataagactaatccctgatagctgacatctccattcatttttatgccatgaaagagctattccagtaactattgattcattacctacagATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAG

Basic information

species Zea mays
transcript GRMZM2G148130_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G148130_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g47770.1 (Oryza sativa), 3'ss of exon 4
tttggatgtaagataagactaatccctgatagctgacatctccattcatttttatgccatgaaag-agctattccagtaactattgattca-ttacctacagATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAG
  ||| |    ||           |||   | ||    |   || | |   |       |||  | || |||     | ||| ||| |||| ||  || ||||||||||||||||||||||||| || || ||||| || |||||| | |||||||| || || || ||| |||| |||||||||||||||
--tgggttctggaatttttgtccacctaccatctttgtttaacaattaacatgtcaatttgaccgcagatatattgtttactgttgtttcacttgtctgcagATATATTGTATGACTCGTGGTCACCGGCGATGACCGTTAGTTCTGTTTGTATCAGTATCTTGTCCATGTTGTCAAGCTCACCAGCAAAG

upper sequence: GRMZM2G148130_T03 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA11G07810.2 (Glycine max), 3'ss of exon 4
------------tttggatgtaagataagactaatccctgatagctgacatctccattcatttttatgccatgaaagagctattccagtaactattgattcattacctacagATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAG--
            |||   | |||  | |||  ||  | ||||   |||| |    | |  |||||     |||   |||||    || | | | | | ||     | | |||||||||||||||| || ||||| || || ||||| || ||||||||||| ||||| ||  | || ||||| || |||||| |  |||||  
gttagccatttttttctttttaaatttagatgaaagcgtgat---tgac-ttggtactggtttttg----atggt-gagctga--catttaatgt-gcttggcatcatgcagATATATTGTATGATTCATGGTCTCCGGCGATGACAGTTAGTTCTATCTGCATCAGTATTCTCTCAATGCTTTCAAGCTCAACCACAAAGGT

upper sequence: GRMZM2G148130_T03 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA11G07810.1 (Glycine max), 3'ss of exon 4
------------tttggatgtaagataagactaatccctgatagctgacatctccattcatttttatgccatgaaagagctattccagtaactattgattcattacctacagATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAG
            |||   | |||  | |||  ||  | ||||   |||| |    | |  |||||     |||   |||||    || | | | | | ||     | | |||||||||||||||| || ||||| || || ||||| || ||||||||||| ||||| ||  | || ||||| || |||||| |  |||||
gttagccatttttttctttttaaatttagatgaaagcgtgat---tgac-ttggtactggtttttg----atggt-gagctga--catttaatgt-gcttggcatcatgcagATATATTGTATGATTCATGGTCTCCGGCGATGACAGTTAGTTCTATCTGCATCAGTATTCTCTCAATGCTTTCAAGCTCAACCACAAAG

upper sequence: GRMZM2G148130_T03 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA01G37480.1 (Glycine max), 3'ss of exon 4
------------tttggatgtaagataagactaatccctgatagctgacatctccattcatttttatgccatgaaagagctattccagtaactattgattcattacctacagATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAG
            |||   | |||  | |||  ||  | ||||   |||| |     ||  |||||  |   |||     |  ||   ||     ||||  ||| |  | |||||||||||||||| || |||||||| || ||||| || ||||||||||| ||||| ||  | || ||||| || |||||| |  |||||
gttaaccatttttttctttttaaatttagataaaagcatgat---tgac-ttggtgttggtttttg-gtggtgagctgacatttgatgtg---cttga--catca--tgcagATATATTGTATGATTCATGGTCCCCTGCGATGACAGTTAGTTCTATCTGCATCAGTATTCTCTCAATGCTTTCAAGCTCAACCACAAAG

upper sequence: GRMZM2G148130_T03 (Zea mays), 3'ss of exon 4
lower sequence: AT1G75440.1 (Arabidopsis thaliana), 3'ss of exon 4
tttggatgtaagat--aagactaatccctgatagc--tgacatctccattcatttttatgccatgaaagagctattccagtaactattgattcattacctacagATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAG
||| | | | ||||  |||  ||  | |  ||  |  |  | | |   || |  |      | || ||||  ||| |   |   |  ||  ||||    | ||||||| |||||||| |||||||| ||||| ||||| || ||||||||||| || |||||  | || ||||| || |||||  | | ||||
ttttgcttttagatccaagggtacactcaaatttcagtagcttattatttaacataggcctcctggaagaagtat-ctgatg--ttgtgtatcatcgt-tgcagATATTTTGTATGATTCGTGGTCTCCAGCCATGACGGTGAGTTCTATCTGCATTAGCATCCTCTCCATGCTCTCAAGCTCGACTGAAAAG

upper sequence: GRMZM2G148130_T03 (Zea mays), 3'ss of exon 4
lower sequence: Vv18s0001g13180.t01 (Vitis vinifera), 3'ss of exon 4
tttggatgtaagataagactaatc--cctgatagctgacatctccattcatttttatgccatgaaagagctattccagtaactattgattcattacct--acagATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAG
   || | | |  | |  |  ||     |   | ||||  ||||  |   |  || | |    | | |   |   |    |  || | ||  ||   |  ||||||||  | ||||| || ||||||||||| ||||| || ||||| ||||||||||||||| | || ||| | || |||||| | |  |||
---ggttcttatttcaatcccattattttatcaactgat-tctctgtggttgattgtccatcaacacactgacatctaatatcatagcttatttgttttcacagATATTCTATATGATTCATGGTCCCCAGCCATGACAGTTAGTTCAATCTGTATCAGCATACTCTCCATGTTATCGAGCTCAACTGTGAAG

upper sequence: GRMZM2G148130_T03 (Zea mays), 3'ss of exon 4
lower sequence: Vv04s0023g02620.t01 (Vitis vinifera), 3'ss of exon 4
--tttggatgtaagataagactaatccctgatagctgacatctcca-ttcatttttatgccatgaaagagctattccagtaactattgattcatt--acctacagATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAG
  | |||||  || ||| |  || |   ||||   |||  |||  |  | | || | | || |  ||     | |    ||  |||||| ||||   |  | ||||||| |||||||| || ||||||||||| ||||| || ||||||||||| ||||||||  | || ||||| || |||||| | |  |||
tttatggatccaa-atatg-ttagtt--tgatta-tgatgtctaaaactaacttatgtacctttcaatctgaaattttatatttattgactcatgtgatgtgcagATATTTTGTATGATTCTTGGTCCCCAGCCATGACAGTTAGTTCTATCTGCATCAGCATTCTCTCCATGCTATCAAGCTCAACTGTGAAG

upper sequence: GRMZM2G148130_T03 (Zea mays), 3'ss of exon 4
lower sequence: PP1S193_49V6.1 (Physcomitrella patens), 3'ss of exon 4
-tttggatgtaagataagactaatccctgatagctgacatctccattcatttttatgccatgaaagagct--attccagtaactattgattcattacctacagATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAG
  |   |      | || |||   | | |  |   |  |      | ||  || |||  ||||      |  ||||  | |  ||||  ||  || |   ||||||||||||||||||| ||||| |||||||||||||| || || ||||| ||||||||  | |||||| | || || ||| |||  |||
aatcatagaatgaagaacactcgacgcagtcatgagggagagtggtgcacgttaatgaaatgatgatttttcattctgggatttatt--tttgtt-caaccagATATATTGTATGACTCTTGGTCACCAGCAATGACTGTGAGCTCCATCTGCATCAGCATCCTCTCTATGTTATCTAGTTCAACAGTGAAG

upper sequence: GRMZM2G148130_T03 (Zea mays), 3'ss of exon 4
lower sequence: PP1S211_21V6.1 (Physcomitrella patens), 3'ss of exon 4
-----tttggatgtaagataagactaatccctgatagctgacatctccattcatttttatgccatgaaagagctattccagtaactattgattcattacctacagATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAG
     ||   |  | |   || ||||   |    ||  |||  |   |||    ||   |   || || ||   ||| | | ||   | | ||| ||  |  |||||||  | |||||||| ||||| ||||||||||| || ||||||||||| ||||||||  | || ||| |||| || ||| | |  |||
acgagttcccaacttaacgaaaactatctctgtgtacttgaatttaacatg---ttgcgtttaattaa-gactaatttctgcaaacttggcttcgtt-tcaccagATATTCTTTATGACTCTTGGTCACCAGCAATGACCGTGAGTTCTATCTGCATCAGCATCCTGTCCATGTTGTCTAGTTCAACTGTGAAG

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|88755064|gb|DY539205.1|DY539205
EST:     CCACACATTTCCAGTAATGGACACATCTGTTTAG                         ATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTA
genomic: CCACACATTTACAGTAATGGACACATCTGTTTAGgtatagccgt ... ttacctacagATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTA
EST: gi|88757761|gb|DY541902.1|DY541902
EST:     TCCAGCCCCGATGCATCCACACATTTACAGTAATGGACACATCTGTTTAG                         ATATATTGTATGACTCGTGGTCCCCACCAATGACTGTCAGTTCTATCTGTA
genomic: TCCAGCACCGATGCATCCACACATTTACAGTAATGGACACATCTGTTTAGgtatagccgt ... ttacctacagATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTA
EST: gi|71427893|gb|DR808943.1|DR808943
EST:     TCCAGCACCGATGCATCCACACATTTACAGTAATGGACACATCTGTTTAG                         ATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTA
genomic: TCCAGCACCGATGCATCCACACATTTACAGTAATGGACACATCTGTTTAGgtatagccgt ... ttacctacagATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTA
EST: gi|89754929|gb|DY685543.1|DY685543
EST:     AGTAATGGACACATCTGTTTAG                         ATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTA
genomic: AGTAATGGACACATCTGTTTAGgtatagccgt ... ttacctacagATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTA
EST: gi|211054652|gb|FL411716.1|FL411716
EST:     TCCAGCACCGATGCATCCACACATTTACAGTAACGGACACATCTGTTTAG                         ATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTA
genomic: TCCAGCACCGATGCATCCACACATTTACAGTAATGGACACATCTGTTTAGgtatagccgt ... ttacctacagATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTA
EST: gi|71445359|gb|DR826409.1|DR826409
EST:     TCCAGCACCGATGCATCCACACATTTACAGTAATGGACACATCTGTTTAG                         ATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTA
genomic: TCCAGCACCGATGCATCCACACATTTACAGTAATGGACACATCTGTTTAGgtatagccgt ... ttacctacagATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTA
EST: gi|71445358|gb|DR826408.1|DR826408
EST:     TCCAGCACCGATGCATCCACACATTTACAGTAATGGACACATCTGTTTAG                         ATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTA
genomic: TCCAGCACCGATGCATCCACACATTTACAGTAATGGACACATCTGTTTAGgtatagccgt ... ttacctacagATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTA
EST: gi|76292123|gb|DV031691.1|DV031691
EST:     TCCAGCACCGATGCATCCACACATTTACAGTAATGGACACATCTGTTTAG                         ATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTA
genomic: TCCAGCACCGATGCATCCACACATTTACAGTAATGGACACATCTGTTTAGgtatagccgt ... ttacctacagATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTA
EST: gi|86475096|gb|DY241466.1|DY241466
EST:     TCCAGCACCGATGCATCCACACATTTACAGTAATGGACACATCTGTTTAG                         ATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTA
genomic: TCCAGCACCGATGCATCCACACATTTACAGTAATGGACACATCTGTTTAGgtatagccgt ... ttacctacagATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTA
EST: gi|84980323|gb|DW530672.1|DW530672
EST:     TCCAGCACCGATGCATCCACACATTTACAGTAATGGACACATCTGTTTAG                         ATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTA
genomic: TCCAGCACCGATGCATCCACACATTTACAGTAATGGACACATCTGTTTAGgtatagccgt ... ttacctacagATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTA
EST: gi|78115399|gb|DV533787.1|DV533787
EST:     TCCAGCACCGATGCATCCACACATTTACAGTAATGGACACATCTGTTTAG                         ATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATTTGTA
genomic: TCCAGCACCGATGCATCCACACATTTACAGTAATGGACACATCTGTTTAGgtatagccgt ... ttacctacagATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTA
EST: gi|211318355|gb|FL450740.1|FL450740
EST:     ATGCATCCACACATTTACAGTAATGGACACATCTGTTTAG                         ATATATTGTATGATTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTA
genomic: ATGCATCCACACATTTACAGTAATGGACACATCTGTTTAGgtatagccgt ... ttacctacagATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatttttatgccatgaaagagctattccagtaactattgattcattacctacagATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAG
                               taactatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttggatgtaagataagactaatccctgatagctgacatctccattcatttttatgccatgaaagagctattccagtaactattgattcattacctacagATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG