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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttggatgtaagataagactaatccctgatagctgacatctccattcatttttatgccatgaaagagctattccagtaactattgattcattacctacagATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAGGTTACATATTT

Basic information

species Zea mays
transcript GRMZM2G148130_T04
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G148130_T04 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g47770.1 (Oryza sativa), 3'ss of exon 4
tttggatgtaagataagactaatccctgatagctgacatctccattcatttttatgccatgaaag-agctattccagtaactattgattca-ttacctacagATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAGGTTACATATTT
  ||| |    ||           |||   | ||    |   || | |   |       |||  | || |||     | ||| ||| |||| ||  || ||||||||||||||||||||||||| || || ||||| || |||||| | |||||||| || || || ||| |||| |||||||||||||||           
--tgggttctggaatttttgtccacctaccatctttgtttaacaattaacatgtcaatttgaccgcagatatattgtttactgttgtttcacttgtctgcagATATATTGTATGACTCGTGGTCACCGGCGATGACCGTTAGTTCTGTTTGTATCAGTATCTTGTCCATGTTGTCAAGCTCACCAGCAAAG-----------

upper sequence: GRMZM2G148130_T04 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA11G07810.2 (Glycine max), 3'ss of exon 4
------------tttggatgtaagataagactaatccctgatagctgacatctccattcatttttatgccatgaaagagctattccagtaactattgattcattacctacagATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAGGTTACATATTT
            |||   | |||  | |||  ||  | ||||   |||| |    | |  |||||     |||   |||||    || | | | | | ||     | | |||||||||||||||| || ||||| || || ||||| || ||||||||||| ||||| ||  | || ||||| || |||||| |  |||||||         
gttagccatttttttctttttaaatttagatgaaagcgtgat---tgac-ttggtactggtttttg----atggt-gagctga--catttaatgt-gcttggcatcatgcagATATATTGTATGATTCATGGTCTCCGGCGATGACAGTTAGTTCTATCTGCATCAGTATTCTCTCAATGCTTTCAAGCTCAACCACAAAGGT---------

upper sequence: GRMZM2G148130_T04 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA11G07810.1 (Glycine max), 3'ss of exon 4
------------tttggatgtaagataagactaatccctgatagctgacatctccattcatttttatgccatgaaagagctattccagtaactattgattcattacctacagATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAGGTTACATATTT
            |||   | |||  | |||  ||  | ||||   |||| |    | |  |||||     |||   |||||    || | | | | | ||     | | |||||||||||||||| || ||||| || || ||||| || ||||||||||| ||||| ||  | || ||||| || |||||| |  |||||           
gttagccatttttttctttttaaatttagatgaaagcgtgat---tgac-ttggtactggtttttg----atggt-gagctga--catttaatgt-gcttggcatcatgcagATATATTGTATGATTCATGGTCTCCGGCGATGACAGTTAGTTCTATCTGCATCAGTATTCTCTCAATGCTTTCAAGCTCAACCACAAAG-----------

upper sequence: GRMZM2G148130_T04 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA01G37480.1 (Glycine max), 3'ss of exon 4
------------tttggatgtaagataagactaatccctgatagctgacatctccattcatttttatgccatgaaagagctattccagtaactattgattcattacctacagATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAGGTTACATATTT
            |||   | |||  | |||  ||  | ||||   |||| |     ||  |||||  |   |||     |  ||   ||     ||||  ||| |  | |||||||||||||||| || |||||||| || ||||| || ||||||||||| ||||| ||  | || ||||| || |||||| |  |||||           
gttaaccatttttttctttttaaatttagataaaagcatgat---tgac-ttggtgttggtttttg-gtggtgagctgacatttgatgtgc---ttga--catca--tgcagATATATTGTATGATTCATGGTCCCCTGCGATGACAGTTAGTTCTATCTGCATCAGTATTCTCTCAATGCTTTCAAGCTCAACCACAAAG-----------

upper sequence: GRMZM2G148130_T04 (Zea mays), 3'ss of exon 3
lower sequence: AT1G75440.1 (Arabidopsis thaliana), 3'ss of exon 4
tttggatgtaagat--aagactaatccctgatagc--tgacatctccattcatttttatgccatgaaagagctattccagtaactattgattcattacctacagATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAGGTTACATATTT
||| | | | ||||  |||  ||  | |  ||  |  |  | | |   || |  |      | || ||||  ||| |   |   |  ||  ||||    | ||||||| |||||||| |||||||| ||||| ||||| || ||||||||||| || |||||  | || ||||| || |||||  | | ||||           
ttttgcttttagatccaagggtacactcaaatttcagtagcttattatttaacataggcctcctggaagaagtat-ctgatg--ttgtgtatcatcgt-tgcagATATTTTGTATGATTCGTGGTCTCCAGCCATGACGGTGAGTTCTATCTGCATTAGCATCCTCTCCATGCTCTCAAGCTCGACTGAAAAG-----------

upper sequence: GRMZM2G148130_T04 (Zea mays), 3'ss of exon 3
lower sequence: Vv18s0001g13180.t01 (Vitis vinifera), 3'ss of exon 4
tttggatgtaagataagactaatc--cctgatagctgacatctccattcatttttatgccatgaaagagctattccagtaactattgattcattacct--acagATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAGGTTACATATTT
   || | | |  | |  |  ||     |   | ||||  ||||  |   |  || | |    | | |   |   |    |  || | ||  ||   |  ||||||||  | ||||| || ||||||||||| ||||| || ||||| ||||||||||||||| | || ||| | || |||||| | |  |||           
---ggttcttatttcaatcccattattttatcaactgat-tctctgtggttgattgtccatcaacacactgacatctaatatcatagcttatttgttttcacagATATTCTATATGATTCATGGTCCCCAGCCATGACAGTTAGTTCAATCTGTATCAGCATACTCTCCATGTTATCGAGCTCAACTGTGAAG-----------

upper sequence: GRMZM2G148130_T04 (Zea mays), 3'ss of exon 3
lower sequence: Vv04s0023g02620.t01 (Vitis vinifera), 3'ss of exon 4
--tttggatgtaagataagactaatccctgatagctgacatctcca-ttcatttttatgccatgaaagagctattccagtaactattgattcatt--acctacagATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAGGTTACATATTT
  | |||||  || ||| |  || |   ||||   |||  |||  |  | | || | | || |  ||     | |    ||  |||||| ||||   |  | ||||||| |||||||| || ||||||||||| ||||| || ||||||||||| ||||||||  | || ||||| || |||||| | |  |||           
tttatggatccaa-atatg-ttagt--ttgatta-tgatgtctaaaactaacttatgtacctttcaatctgaaattttatatttattgactcatgtgatgtgcagATATTTTGTATGATTCTTGGTCCCCAGCCATGACAGTTAGTTCTATCTGCATCAGCATTCTCTCCATGCTATCAAGCTCAACTGTGAAG-----------

upper sequence: GRMZM2G148130_T04 (Zea mays), 3'ss of exon 3
lower sequence: PP1S193_49V6.1 (Physcomitrella patens), 3'ss of exon 4
-tttggatgtaagataagactaatccctgatagctgacatctccattcatttttatgccatgaaagagct--attccagtaactattgattcattacctacagATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAGGTTACATATTT
  |   |      | || |||   | | |  |   |  |      | ||  || |||  ||||      |  ||||  | |  ||||  ||  || |   ||||||||||||||||||| ||||| |||||||||||||| || || ||||| ||||||||  | |||||| | || || ||| |||  |||           
aatcatagaatgaagaacactcgacgcagtcatgagggagagtggtgcacgttaatgaaatgatgatttttcattctgggatttatt--tttgtt-caaccagATATATTGTATGACTCTTGGTCACCAGCAATGACTGTGAGCTCCATCTGCATCAGCATCCTCTCTATGTTATCTAGTTCAACAGTGAAG-----------

upper sequence: GRMZM2G148130_T04 (Zea mays), 3'ss of exon 3
lower sequence: PP1S211_21V6.1 (Physcomitrella patens), 3'ss of exon 4
-----tttggatgtaagataagactaatccctgatagctgacatctccattcatttttatgccatgaaagagctattccagtaactattgattcattacctacagATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAGGTTACATATTT
     ||   |  | |   || ||||   |    ||  |||  |   |||    ||   |   || || ||   ||| | | ||   | | ||| ||  |  |||||||  | |||||||| ||||| ||||||||||| || ||||||||||| ||||||||  | || ||| |||| || ||| | |  |||           
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|88757762|gb|DY541903.1|DY541903
EST:     TCCAGCACCGATGCATCCACACATTTACAGTAATGGACACATCTGTTTAG                         ATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTA
genomic: TCCAGCACCGATGCATCCACACATTTACAGTAATGGACACATCTGTTTAGgtatagccgt ... ttacctacagATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTA
EST: gi|93282265|gb|EB674529.1|EB674529
EST:     TCCAGCACCGATGCATCCACACATTTACAGTAATGGACACATCTGTTTAG                         ATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTA
genomic: TCCAGCACCGATGCATCCACACATTTACAGTAATGGACACATCTGTTTAGgtatagccgt ... ttacctacagATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTA
EST: gi|76289947|gb|DV029515.1|DV029515
EST:     TCCAGCACCGATGCATCCACACATTTACAGTAATGGACACATCTGTTTAG                         ATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTA
genomic: TCCAGCACCGATGCATCCACACATTTACAGTAATGGACACATCTGTTTAGgtatagccgt ... ttacctacagATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTA
EST: gi|78092977|gb|DV521351.1|DV521351
EST:     TCCAGCACCGATGCATCCACACATTTACAGTAATGGACACATCTGTTTAG                         ATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTA
genomic: TCCAGCACCGATGCATCCACACATTTACAGTAATGGACACATCTGTTTAGgtatagccgt ... ttacctacagATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTA
EST: gi|86475097|gb|DY241467.1|DY241467
EST:     TCCAGCACCGATGCATCCACACATTTACAGTAATGGACACATCTGTTTAG                         ATATATTGTATGACTC
genomic: TCCAGCACCGATGCATCCACACATTTACAGTAATGGACACATCTGTTTAGgtatagccgt ... ttacctacagATATATTGTATGACTC
EST: gi|76012087|gb|DT939257.1|DT939257
EST:     TCCAGCACCGATGCATCCACACATTTACAGTAATGGACACATCTGTTTAG                         ATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTA
genomic: TCCAGCACCGATGCATCCACACATTTACAGTAATGGACACATCTGTTTAGgtatagccgt ... ttacctacagATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatttttatgccatgaaagagctattccagtaactattgattcattacctacagATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAGGTTACATATTT
                               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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttggatgtaagataagactaatccctgatagctgacatctccattcatttttatgccatgaaagagctattccagtaactattgattcattacctacagATATATTGTATGACTCGTGGTCCCCAGCAATGACTGTCAGTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCACCAGCAAAGGTTACATATTT

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