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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atggcaacttatataatgtaaagttctttttgtggttgagagtcatagtatttggtggcttctacagtcgttaattagtcctgttttagtgaatttgaagAGGTGGAAGCAGCACCTGTGTTGGTTGATGGCCCTCTAGAACCGCAAACGTCAAATATCATGTCAACTACTACTCACATTCAAGAGGATCCTTTATCTGC

Basic information

species Zea mays
transcript GRMZM2G144618_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G144618_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os07g14580.1 (Oryza sativa), 3'ss of exon 5
---atggcaacttata----taatgtaaagttctt---tttgtggttgagagtcatagtatt-tggtggcttctacagtcgttaattagtcctgttttagtgaatttgaagAGGTGGAAGCAGCACCTGTGTTGGTTGATGGCCCTCTAGAACCGCAAACGTCAAATATCATGTCAACTACTACTCACATTCAAGAGGATCCTTTATCTGC
   || | ||   ||     |||| |   | | ||   | | |  |||  |   |   | || | ||         |  |  | ||   || | ||| ||||||||||||||| ||||||||||||||   |||||||| || || ||||| || ||||| || ||||||||  || ||||||| ||  | || ||||||           
tgtattgtaaaccattcccttaatttgttgcttttgaatgtatatttgccataaactatgttattgtaatagtgttatactgtcatcgatcttatttcagTGAATTTGAAGAGCTGGAAGCAGCACCTACTTTGGTTGAAGGTCCACTAGAGCCTCAAACATCGAATATCATACCAGCTACTACCCATGTCCAGGAGGAT-----------
















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|50322552|gb|CO517678.1|CO517678
EST:     AATGCTTTCTCGAAGGTGCCACCAAAGCCGAAGATTCCCCCTGTTCAAAG                         T
genomic: AATGCTTTCTCGAAGGTGCCACCAAAGCCGAAGATTCCCCCTGTTCAAAGgtaattggaa ... gaatttgaag-
EST: gi|50322552|gb|CO517678.1|CO517678
EST:     AATGCTTTCTCGAAGGTGCCACCAAAGCCGAAGATTCCCCCTGTTCAAAG                         T
genomic: AATGCTTTCTCGAAGGTGCCACCAAAGCCGAAGATTCCCCCTGTTCAAAGgtaattggaa ... gaatttgaag-
EST: gi|50322552|gb|CO517678.1|CO517678
EST:     AATGCTTTCTCGAAGGTGCCACCAAAGCCGAAGATTCCCCCTGTTCAAAG                         T
genomic: AATGCTTTCTCGAAGGTGCCACCAAAGCCGAAGATTCCCCCTGTTCAAAGgtaattggaa ... gaatttgaag-
EST: gi|50322824|gb|CO517950.1|CO517950
EST:     AATGCTTTCTCGAAGGTGCCACCAAAGCCGAAGATTCCCCCTGTTCAAAG                         T
genomic: AATGCTTTCTCGAAGGTGCCACCAAAGCCGAAGATTCCCCCTGTTCAAAGgtaattggaa ... gaatttgaag-
EST: gi|50322824|gb|CO517950.1|CO517950
EST:     AATGCTTTCTCGAAGGTGCCACCAAAGCCGAAGATTCCCCCTGTTCAAAG                         T
genomic: AATGCTTTCTCGAAGGTGCCACCAAAGCCGAAGATTCCCCCTGTTCAAAGgtaattggaa ... gaatttgaag-
EST: gi|50322824|gb|CO517950.1|CO517950
EST:     AATGCTTTCTCGAAGGTGCCACCAAAGCCGAAGATTCCCCCTGTTCAAAG                         T
genomic: AATGCTTTCTCGAAGGTGCCACCAAAGCCGAAGATTCCCCCTGTTCAAAGgtaattggaa ... gaatttgaag-
EST: gi|71448550|gb|DR829600.1|DR829600
EST:     AATGCTTTCTCGAAGGTGCCACCAAAGCCGAAGATTCCCCCTGTTCAAAG                         T
genomic: AATGCTTTCTCGAAGGTGCCACCAAAGCCGAAGATTCCCCCTGTTCAAAGgtaattggaa ... gaatttgaag-
EST: gi|71448550|gb|DR829600.1|DR829600
EST:     AATGCTTTCTCGAAGGTGCCACCAAAGCCGAAGATTCCCCCTGTTCAAAG                         T
genomic: AATGCTTTCTCGAAGGTGCCACCAAAGCCGAAGATTCCCCCTGTTCAAAGgtaattggaa ... gaatttgaag-
EST: gi|71448550|gb|DR829600.1|DR829600
EST:     AATGCTTTCTCGAAGGTGCCACCAAAGCCGAAGATTCCCCCTGTTCAAAG                         T
genomic: AATGCTTTCTCGAAGGTGCCACCAAAGCCGAAGATTCCCCCTGTTCAAAGgtaattggaa ... gaatttgaag-
EST: gi|89761719|gb|DY689622.1|DY689622
EST:     AATGCTTTCTCGAAGGTGCCACCAAAGCCGAAGATTCCCCCTGTTCAAAG                         T
genomic: AATGCTTTCTCGAAGGTGCCACCAAAGCCGAAGATTCCCCCTGTTCAAAGgtaattggaa ... gaatttgaag-
EST: gi|89761719|gb|DY689622.1|DY689622
EST:     AATGCTTTCTCGAAGGTGCCACCAAAGCCGAAGATTCCCCCTGTTCAAAG                         T
genomic: AATGCTTTCTCGAAGGTGCCACCAAAGCCGAAGATTCCCCCTGTTCAAAGgtaattggaa ... gaatttgaag-
EST: gi|89761719|gb|DY689622.1|DY689622
EST:     AATGCTTTCTCGAAGGTGCCACCAAAGCCGAAGATTCCCCCTGTTCAAAG                         T
genomic: AATGCTTTCTCGAAGGTGCCACCAAAGCCGAAGATTCCCCCTGTTCAAAGgtaattggaa ... gaatttgaag-
EST: gi|71443863|gb|DR824913.1|DR824913
EST:     AATGCTTTCTCGAAGGTGCCACCAAAGCCGAAGATTCCCCCTGTTCAAAG                         T
genomic: AATGCTTTCTCGAAGGTGCCACCAAAGCCGAAGATTCCCCCTGTTCAAAGgtaattggaa ... gaatttgaag-
EST: gi|71443863|gb|DR824913.1|DR824913
EST:     AATGCTTTCTCGAAGGTGCCACCAAAGCCGAAGATTCCCCCTGTTCAAAG                         T
genomic: AATGCTTTCTCGAAGGTGCCACCAAAGCCGAAGATTCCCCCTGTTCAAAGgtaattggaa ... gaatttgaag-
EST: gi|71443863|gb|DR824913.1|DR824913
EST:     AATGCTTTCTCGAAGGTGCCACCAAAGCCGAAGATTCCCCCTGTTCAAAG                         T
genomic: AATGCTTTCTCGAAGGTGCCACCAAAGCCGAAGATTCCCCCTGTTCAAAGgtaattggaa ... gaatttgaag-
EST: gi|93012223|gb|EB637743.1|EB637743
EST:     AATGCTTTCTCGAAGGTGCCACCAAAGCCGAAGATTCCCCCTGTTCAAAG                         AGGTGGAAGCAGCACCTGTGTTGGTTGATGGCCCTCTAGAACCGCAAACGT
genomic: AATGCTTTCTCGAAGGTGCCACCAAAGCCGAAGATTCCCCCTGTTCAAAGgtaattggaa ... gaatttgaagAGGTGGAAGCAGCACCTGTGTTGGTTGATGGCCCTCTAGAACCGCAAACGT
EST: gi|76286410|gb|DV025978.1|DV025978
EST:     AATGCTTTCTCGAAGGTGCCACCAAAGCCGAAGATTCCCCCTGTTCAAAG                         T
genomic: AATGCTTTCTCGAAGGTGCCACCAAAGCCGAAGATTCCCCCTGTTCAAAGgtaattggaa ... gaatttgaag-
EST: gi|76286410|gb|DV025978.1|DV025978
EST:     AATGCTTTCTCGAAGGTGCCACCAAAGCCGAAGATTCCCCCTGTTCAAAG                         T
genomic: AATGCTTTCTCGAAGGTGCCACCAAAGCCGAAGATTCCCCCTGTTCAAAGgtaattggaa ... gaatttgaag-
EST: gi|76286410|gb|DV025978.1|DV025978
EST:     AATGCTTTCTCGAAGGTGCCACCAAAGCCGAAGATTCCCCCTGTTCAAAG                         T
genomic: AATGCTTTCTCGAAGGTGCCACCAAAGCCGAAGATTCCCCCTGTTCAAAGgtaattggaa ... gaatttgaag-
EST: gi|149014053|gb|EE043578.2|EE043578
EST:     AATGCTTTCTCGAAGGTGCCACCAAAGCCGAAGATTCCCCCTGTTCAAAG                         T
genomic: AATGCTTTCTCGAAGGTGCCACCAAAGCCGAAGATTCCCCCTGTTCAAAGgtaattggaa ... gaatttgaag-
EST: gi|149014053|gb|EE043578.2|EE043578
EST:     AATGCTTTCTCGAAGGTGCCACCAAAGCCGAAGATTCCCCCTGTTCAAAG                         T
genomic: AATGCTTTCTCGAAGGTGCCACCAAAGCCGAAGATTCCCCCTGTTCAAAGgtaattggaa ... gaatttgaag-
EST: gi|149014053|gb|EE043578.2|EE043578
EST:     AATGCTTTCTCGAAGGTGCCACCAAAGCCGAAGATTCCCCCTGTTCAAAG                         T
genomic: AATGCTTTCTCGAAGGTGCCACCAAAGCCGAAGATTCCCCCTGTTCAAAGgtaattggaa ... gaatttgaag-
EST: gi|76017159|gb|DT944329.1|DT944329
EST:     AATGCTTTCTCGAAGGTGCCACCAAAGCCGAAGATTCCCCCTGTTCAAAG                         T
genomic: AATGCTTTCTCGAAGGTGCCACCAAAGCCGAAGATTCCCCCTGTTCAAAGgtaattggaa ... gaatttgaag-
EST: gi|76017159|gb|DT944329.1|DT944329
EST:     AATGCTTTCTCGAAGGTGCCACCAAAGCCGAAGATTCCCCCTGTTCAAAG                         T
genomic: AATGCTTTCTCGAAGGTGCCACCAAAGCCGAAGATTCCCCCTGTTCAAAGgtaattggaa ... gaatttgaag-
EST: gi|76017159|gb|DT944329.1|DT944329
EST:     AATGCTTTCTCGAAGGTGCCACCAAAGCCGAAGATTCCCCCTGTTCAAAG                         T
genomic: AATGCTTTCTCGAAGGTGCCACCAAAGCCGAAGATTCCCCCTGTTCAAAGgtaattggaa ... gaatttgaag-


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtatttggtggcttctacagtcgttaattagtcctgttttagtgaatttgaagAGGTGGAAGCAGCACCTGTGTTGGTTGATGGCCCTCTAGAACCGCAAACGTCAAATATCATGTCAACTACTACTCACATTCAAGAGGATCCTTTATCTGC
                       cgttaat  putative branch site (score: 4)
                         ttaattagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atggcaacttatataatgtaaagttctttttgtggttgagagtcatagtatttggtggcttctacagtcgttaattagtcctgttttagtgaatttgaagAGGTGGAAGCAGCACCTGTGTTGGTTGATGGCCCTCTAGAACCGCAAACGTCAAATATCATGTCAACTACTACTCACATTCAAGAGGATCCTTTATCTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - -gtggttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ggcttct