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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaactattactgttgttgtttatccctgtacttttgaattgtggggctaggactaaagtttgaccacttatacttccatcacagATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTG

Basic information

species Zea mays
transcript GRMZM2G032367_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G032367_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os05g23620.1 (Oryza sativa), 3'ss of exon 7
gtaaactattactgttgttgtttatccct-gtacttttgaattgtggggctaggactaa-------agtttgaccacttata-cttccatcacagATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTG
||||  |  || ||  ||||||   | ||   | || |||  ||| ||| ||| | |||       ||  |||    |   | | || | |||||||||| |||||||| || || ||| | |||||||||||||| ||||||||||||||||| || |||
gtaagtttctaatgc-gttgttgggctcttacagttgtgacatgttgggttagcattaagggcctaagcatgattgttgtcatcctctaccacagATGGGCAAGGATGTCGTTTCGTTCTTGTCATGGGCAGCTGAACCTGAGATGGAAGAGAGGAAACTG

upper sequence: GRMZM2G032367_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA05G07020.1 (Glycine max), 3'ss of exon 6
----------------gtaaactattactgttgttgtttatccctg---tacttttgaattgtgg--ggctaggactaaa-gtttgaccacttatacttccatcacagATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTG
                   ||   || | ||   | |     | ||   ||  | |||| | |||  |  |   || |||   ||      ||||| ||     |||||||||||| ||  |||||||||||||  | ||||| || || |||||||||||||||||||| |||
gtacttttgtttgttgaggaatggtttcagtaaatctcatcacatggattatctatgaactttggaagaattatacgaaataattttttggttata-ttttgctacagATGGGTAAAGACATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATGGAAGAGAGAAAACTG

upper sequence: GRMZM2G032367_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA19G22530.2 (Glycine max), 3'ss of exon 6
-----------------------------gtaaactattactgttgttgtttatccctgtacttttgaattgtggggctaggactaaagtttgaccacttatacttccatcacagATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTG
                             |||||    |  ||   ||| |||||  || ||||  |||   |   || |  |   |  ||||   ||||     |     |||||||||||| ||| |||||||||||||  | ||||| || || |||||||||||||||||||| |||
gtacctttatttgttgaggagtggtttcagtaaatc--tcatgacattgattatctatgaacttcggaaaaattatgc-aaaatatatttttggttactt-----tttgctacagATGGGTAAAGATATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATGGAAGAGAGAAAACTG

upper sequence: GRMZM2G032367_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA16G06700.2 (Glycine max), 3'ss of exon 6
---gtaaact-attactgttgttgtttatccctgta---cttttgaattgtggggctag---gactaaagtttgaccacttatact-tccatcacagATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTG
    |||| |   | |||  |   | |      |||   ||| | ||   ||||  | |   || |  || |      ||  || | |   |  |||||||| ||||||||||| |||||| |  | ||||| || || || ||||||||||||||||| |||
gtattaaatttgcttctggaggaatatggtttagtaaatcttcttaaaaatgggatttgatagaatctagctcattttctcttaatgtttgttgcagATGGGGAAGGATGTTGTGTCATTCTTAACTTGGGCCGCCGAACCCGAGATGGAAGAGAGAAAACTG

upper sequence: GRMZM2G032367_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA19G24620.2 (Glycine max), 3'ss of exon 6
-------gtaaactattactgttgttgttta-tccctgtacttttgaattgtgg--ggctaggactaaagtttgaccacttatacttccatcacagATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTG
        |    |  |   |   | ||||| |   | | |||   ||| |     ||  |  |   |  |      | ||  |  |   |  |||||||| ||||||||||| |||||| |    ||||| || || |||||||||||||||||||| |||
gtattatatttgtttctggaggaatggtttagtaaatcttcttacaaatagaaattggaaaaaatgtagctcattttattttaatgtttgttgcagATGGGGAAGGATGTTGTGTCATTCTTAAGTTGGGCCGCCGAACCTGAGATGGAAGAGAGAAAACTG

upper sequence: GRMZM2G032367_T03 (Zea mays), 3'ss of exon 6
lower sequence: AT3G27240.1 (Arabidopsis thaliana), 3'ss of exon 6
----------------gtaaactattac--tgttgttgtttat-ccctgtacttttgaattgtggggctaggactaaagtttgaccacttatacttccatcacagATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTG
                 |||| ||| |     |   | ||||| || | |  |  ||   | |      ||    |   | | |  ||||    || |    ||||||||||| ||| ||||||||||| |  | ||||||||||| || || ||||||||||| || |||
gttatttttcctccacttaaaatataagaacataaatctttatgccttatggtactgtccttt---ctcagtgtcatgatataa--actttactttacggtgcagATGGGTAAAGATATTGTATCATTCTTGGCCTGGGCAGCTGAACCAGAAATGGAAGAGAGGAAACTG

upper sequence: GRMZM2G032367_T03 (Zea mays), 3'ss of exon 6
lower sequence: AT5G40810.2 (Arabidopsis thaliana), 3'ss of exon 5
-------------------------------gtaaactattac-tgttgttgtttatccctgtacttttgaattgtggggctaggactaaagtttgaccacttatacttccatca--cagATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTG
                               | | || || |  | || |    | |  |  | | | ||| |        ||    | || |||      ||  |    ||| |  ||||||||||| ||||||||||| ||| | || ||||||||||| || |||||||||||||| ||  ||
gttagttttcctctgcttaagaaaataatttgcagaccataaagttttatcagatttgacctttcctctgagtcaattatataatctttaatttttctttttttaaaaaacatgatgcagATGGGTAAAGATGTTGTATCCTTCTTGTCCTGGGCAGCTGAACCAGAGATGGAAGAGAGGAAATTG

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|71331562|gb|DR802627.1|DR802627
EST:     ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAG                         ATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
genomic: ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAGgtaaactatt ... tccatcacagATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
EST: gi|5006059|gb|AI712121.1|AI712121
EST:     ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAG                         ATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
genomic: ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAGgtaaactatt ... tccatcacagATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
EST: gi|60347964|gb|DN214937.1|DN214937
EST:     ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAG                         ATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
genomic: ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAGgtaaactatt ... tccatcacagATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
EST: gi|30705061|gb|CD058656.1|CD058656
EST:     ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAG                         ATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGA
genomic: ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAGgtaaactatt ... tccatcacagATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGA
EST: gi|50338206|gb|CO533332.1|CO533332
EST:     ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAG                         ATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
genomic: ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAGgtaaactatt ... tccatcacagATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
EST: gi|14245130|gb|BG873712.1|BG873712
EST:     ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAG                         ATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
genomic: ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAGgtaaactatt ... tccatcacagATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
EST: gi|76290228|gb|DV029796.1|DV029796
EST:     ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAG                         ATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
genomic: ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAGgtaaactatt ... tccatcacagATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
EST: gi|32938109|gb|CF042928.1|CF042928
EST:     CCTGCAACTGAAGCCCAG                         ATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
genomic: CCTGCAACTGAAGCCCAGgtaaactatt ... tccatcacagATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
EST: gi|76016444|gb|DT943614.1|DT943614
EST:     ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAG                         ATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
genomic: ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAGgtaaactatt ... tccatcacagATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
EST: gi|71757789|gb|DR955726.1|DR955726
EST:     ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAG                         ATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
genomic: ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAGgtaaactatt ... tccatcacagATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
EST: gi|78108501|gb|DV526919.1|DV526919
EST:     ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAG                         ATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTG
genomic: ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAGgtaaactatt ... tccatcacagATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTG
EST: gi|74239656|gb|DT647570.1|DT647570
EST:     ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAG                         ATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
genomic: ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAGgtaaactatt ... tccatcacagATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
EST: gi|5608164|gb|AI901831.1|AI901831
EST:     AGTATGAGGATGGTACTCCTGCAACTGAAGCCCAG                         ATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
genomic: AGTATGAGGATGGTACTCCTGCAACTGAAGCCCAGgtaaactatt ... tccatcacagATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
EST: gi|78026464|gb|DV494851.1|DV494851
EST:     ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAG                         ATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
genomic: ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAGgtaaactatt ... tccatcacagATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
EST: gi|37386374|gb|CF630373.1|CF630373
EST:     ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAG                         ATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
genomic: ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAGgtaaactatt ... tccatcacagATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
EST: gi|32939220|gb|CF044039.1|CF044039
EST:     CCTGCAACTGAAGCCCAG                         ATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
genomic: CCTGCAACTGAAGCCCAGgtaaactatt ... tccatcacagATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
EST: gi|101393980|gb|EB818923.1|EB818923
EST:     ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAG                         ATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
genomic: ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAGgtaaactatt ... tccatcacagATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
EST: gi|29947382|gb|CB816627.1|CB816627
EST:     ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAG                         ATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
genomic: ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAGgtaaactatt ... tccatcacagATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
EST: gi|91878166|gb|EB408123.1|EB408123
EST:     ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAG                         ATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
genomic: ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAGgtaaactatt ... tccatcacagATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
EST: gi|211323657|gb|FL286663.1|FL286663
EST:     ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAG                         ATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
genomic: ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAGgtaaactatt ... tccatcacagATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
EST: gi|14206642|gb|BG840320.1|BG840320
EST:     ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAG                         ATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG
genomic: ATGATGGAGCTGTTGAGTATGAGGATGGTACTCCTGCAACTGAAGCCCAGgtaaactatt ... tccatcacagATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttttgaattgtggggctaggactaaagtttgaccacttatacttccatcacagATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTG
                                           cttccatc  CT-rich tract
                        taaagttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaactattactgttgttgtttatccctgtacttttgaattgtggggctaggactaaagtttgaccacttatacttccatcacagATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG