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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggaccttcccatctgcacctcatgttcattctcttttgatgttctcaattttgcaaaaaacaaaaacaaaaacacagGAGTGGATCATGGAACAATGGGATAAAAGTTTCTACATCAGTTCTGTTGCTGGCTCCAACAATGGAAGTTCTATTGTAGTGATGTCAAAAG

Basic information

species Zea mays
transcript GRMZM2G017835_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017835_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA20G38770.1 (Glycine max), 3'ss of exon 12
gtaggaccttcccatctgcacctca---tgttcattctcttttgatgttctcaattttgcaaaaaacaaaaacaaaaacacagGAGTGGATCATGGAACAATGGGATAAAAGTTTCTACATCAGTTCTGTTGCTGGCTCCAACAATGGAAGTTCTATTGTAGTGATGTCAAAAG
||   |  | |   | ||     ||   | || | |||  ||  ||||  | ||  ||    |     |           ||||| ||||| ||||| || ||||||||||  || ||||||| |||| |||| ||   ||||||||| || ||| |||| |||||||||||||
gtgaaatatgct-gtatgtcttgcagtttctttaatctaattccatgtgattaaaattatccatg-tgactgttgctttgcagGAATGGATTATGGAGCAGTGGGATAAAAACTTTTACATCACTTCTATTGCAGGGAGCAACAATGGCAGCTCTCTTGTGGTGATGTCAAAAG

upper sequence: GRMZM2G017835_T01 (Zea mays), 3'ss of exon 11
lower sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 12
-----------------gtaggaccttcccatctgcacctcatgttcattctcttttgatgttctcaattttgcaaaa-aacaaaaacaaaaaca-----cagGAGTGGATCATGGAACAATGGGATAAAAGTTTCTACATCAGTTCTGTTGCTGGCTCCAACAATGGAAGTTCTATTGTAGTGATGTCAAAAG
                 ||      || |    ||    |  ||     |||  || |   |  ||  || || |||  ||||    ||     |     |||||||||||||||||||| ||||| || | |||||| |||||| |  |||||||  | || ||||| || ||| | || || ||||| ||||
gtaagtgctcagtgattgtttagtgtttctgcttgttgtttttgaaggatctagttggccctcttcttttgtggaaattaacatggtcattggtattctacagGAGTGGATCATGGAACAGTGGGAAAAGAATTTCTATATCAGTGCAATTGCTGGAGCTAATAATGGGAGCTCTTTGGTCGTCATGTCGAAAG

upper sequence: GRMZM2G017835_T01 (Zea mays), 3'ss of exon 11
lower sequence: PP1S131_16V6.1 (Physcomitrella patens), 3'ss of exon 12
-------------------------------gtaggaccttcccatctgcacctcatgtt----cattctcttttgatgttctcaattttgcaaaaaacaaaaacaaaaacacagGAGTGGATCATGGAACAATGGGATAAAAGTTTCTACATCAGTTCTGTTGCTGGCTCCAACAATGGAAGTTCTATTGTAGTGATGTCAAAAG
                               |||| |  | |   |   |     ||| |    ||        || | | | | ||      | |   |   | |     ||||||||||||||||||||| ||||| || | |||||| |||||| |  | |||||  | || || ||||| ||  | || || ||||| ||||
gtgggtgtgtggtgtctcgctcaagttttgggtagtatatgcagcttgtcgttcaatgatagaacagctatccctgttatgcgccatgccctcacattgagtcatatttttacagGAGTGGATCATGGAACAGTGGGAAAAGAATTTCTATATCAGTGCCATCGCTGGTGCAAATAACGGAAGCTCCTTGGTCGTCATGTCTAAAG

upper sequence: GRMZM2G017835_T01 (Zea mays), 3'ss of exon 11
lower sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 10
gtaggaccttcccatctgcacctcatgttcattctcttttgatgttctcaattttgcaaaaaacaaaaacaaaaacacagGAGTGGATCATGGAACAATGGGATAAAAGTTTCTACATCAGTTCTGTTGCTGGCTCCAACAATGGAAGTTCTATTGTAGTGATGTCAAAAG
                          |||    |   ||   |    | | |  |    | | |  |  |       |||||||||||||||||||||||||| ||||  |||||||| ||| |  |||| ||  ||||||| || || ||  | || || ||||||||||
--------------------------gttagcacatcttgcttaactttagtaatcttcatagctcattctcctcggcagGAGTGGATCATGGAACAATGGGAGAAAAACTTCTACATTAGTGCCATTGCAGGAGCCAACAACGGCAGCTCGCTGGTTGTCATGTCAAAAG

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|6020774|gb|AW065582.1|AW065582
EST:     CTGGCTTCTCAGCTCAAGTTTATGAGCTATCTTCACACTTTCTTCATAAG                         GAGTGGATCATGGAACAATGGGATAAAAGTTTCTACATCAGTTCTGTTGCT
genomic: CTGGCTTCTCAGCTCAAGTTTATGAGCTATCTTCACACTTTCTTCATAAGgtaggacctt ... aaaaacacagGAGTGGATCATGGAACAATGGGATAAAAGTTTCTACATCAGTTCTGTTGCT
EST: gi|67011551|gb|CO440300.1|CO440300
EST:     CTGGCTTCTCAGCTCAAGTTTATGAGCTATCTTCACACTTTCTTCATAAG                         GAGTGGATCATGGAACAATGGGATAAAAGTTTCTACATCAGTTCTGTTGCT
genomic: CTGGCTTCTCAGCTCAAGTTTATGAGCTATCTTCACACTTTCTTCATAAGgtaggacctt ... aaaaacacagGAGTGGATCATGGAACAATGGGATAAAAGTTTCTACATCAGTTCTGTTGCT
EST: gi|213179378|gb|FM182943.1|FM182943
EST:     GAGCTATCTTCACACTTTCTTCATAAG                         GAGTGGATCATGGAACAATGGGATAAAAGTTTCTACATCAGTTCTGTTGCT
genomic: GAGCTATCTTCACACTTTCTTCATAAGgtaggacctt ... aaaaacacagGAGTGGATCATGGAACAATGGGATAAAAGTTTCTACATCAGTTCTGTTGCT
EST: gi|148939515|gb|EC884103.2|EC884103
EST:     CTGGCTTCTCAGCTCAAGTTTATGAGCTATCTTCACACTTTCTTCATAAG                         GAGTGGATCATGGAACAATGGGATAAAAGTTTCTACATCAGTTCTGTTGCT
genomic: CTGGCTTCTCAGCTCAAGTTTATGAGCTATCTTCACACTTTCTTCATAAGgtaggacctt ... aaaaacacagGAGTGGATCATGGAACAATGGGATAAAAGTTTCTACATCAGTTCTGTTGCT
EST: gi|6020754|gb|AW065562.1|AW065562
EST:     CTGGCTTCTCAGCTCAAGTTTATGAGCTATCTTCACACTTTCTTCATAAG                         GAGTGGATCATGGAACAATGGGATAAAAGTTTCTACATCAGTTCTGTTGCT
genomic: CTGGCTTCTCAGCTCAAGTTTATGAGCTATCTTCACACTTTCTTCATAAGgtaggacctt ... aaaaacacagGAGTGGATCATGGAACAATGGGATAAAAGTTTCTACATCAGTTCTGTTGCT
EST: gi|76285883|gb|DV025451.1|DV025451
EST:     CTGGCTTCTCAGCTCAAGTTTATGAGCTATCTTCACACTTTCTTCATAAG                         GAGTGGATCATGGAACAATGGGATAAAAGTTTCTACATCAGTTCTGTTGCT
genomic: CTGGCTTCTCAGCTCAAGTTTATGAGCTATCTTCACACTTTCTTCATAAGgtaggacctt ... aaaaacacagGAGTGGATCATGGAACAATGGGATAAAAGTTTCTACATCAGTTCTGTTGCT
EST: gi|38568968|gb|CF974853.1|CF974853
EST:     CTGGCTTCTCAGCTCAAGTTTATGAGCTATCTTCACACTTTCTTCATAAG                         GAGTGGATCATGGAACAATGGGATAAAAGTTTCTACATCAGTTCTGTTGCT
genomic: CTGGCTTCTCAGCTCAAGTTTATGAGCTATCTTCACACTTTCTTCATAAGgtaggacctt ... aaaaacacagGAGTGGATCATGGAACAATGGGATAAAAGTTTCTACATCAGTTCTGTTGCT
EST: gi|67025680|gb|CO454429.1|CO454429
EST:     CTGGCTTCTCAGCTCAAGTTTATGAGCTATCTTCACACTTTCTTCATAAG                         GAGTGGATCATGGAACAATGGGATAAAAGTTTCTACATCAGTTCTGTTGCT
genomic: CTGGCTTCTCAGCTCAAGTTTATGAGCTATCTTCACACTTTCTTCATAAGgtaggacctt ... aaaaacacagGAGTGGATCATGGAACAATGGGATAAAAGTTTCTACATCAGTTCTGTTGCT
EST: gi|67025667|gb|CO454416.1|CO454416
EST:     CTGGCTTCTCAGCTCAAGTTTATGAGCTATCTTCACACTTTCTTCATAAG                         GAGTGGATCATGGAACAATGGGATAAAAGTTTCTACATCAGTTCTGTTGCT
genomic: CTGGCTTCTCAGCTCAAGTTTATGAGCTATCTTCACACTTTCTTCATAAGgtaggacctt ... aaaaacacagGAGTGGATCATGGAACAATGGGATAAAAGTTTCTACATCAGTTCTGTTGCT
EST: gi|67011858|gb|CO440607.1|CO440607
EST:     CTGGCTTCTCAGCTCAAGTTTATGAGCTATCTTCACACTTTCTTCATAAG                         GAGTGGATCATGGAACAATGGGAT-AAAGTTTCTACATCAGTTCTGTTGCT
genomic: CTGGCTTCTCAGCTCAAGTTTATGAGCTATCTTCACACTTTCTTCATAAGgtaggacctt ... aaaaacacagGAGTGGATCATGGAACAATGGGATAAAAGTTTCTACATCAGTTCTGTTGCT
EST: gi|113702247|gb|EE679751.1|EE679751
EST:     CTGGCTTCTCAGCTCAAGTTTATGAGCTATCTTCACACTTTCTTCATAAG                         GAGTGGATCATGGAACAATGGGATAAAAGTTTCTACATCAGTTCTGTTGCT
genomic: CTGGCTTCTCAGCTCAAGTTTATGAGCTATCTTCACACTTTCTTCATAAGgtaggacctt ... aaaaacacagGAGTGGATCATGGAACAATGGGATAAAAGTTTCTACATCAGTTCTGTTGCT
EST: gi|14204221|gb|BG837898.1|BG837898
EST:     CTGGCTTCTCAGCTCAAGTTTATGAGCTATCTTCACACTTTCTTCATAAG                         GAGTGGATCATGGAACAATGGGATAAAAGTTTCTACATCAGTTCTGTTGCT
genomic: CTGGCTTCTCAGCTCAAGTTTATGAGCTATCTTCACACTTTCTTCATAAGgtaggacctt ... aaaaacacagGAGTGGATCATGGAACAATGGGATAAAAGTTTCTACATCAGTTCTGTTGCT
EST: gi|33101699|gb|CF061659.1|CF061659
EST:     CTGGCTTCTCAGCTCAAGTTTATGAGCTATCTTCACACTTTCTTCATAAG                         GAGTGGATCATGGAACAATGGGATAAAAGTTTCTACATCAGTTCTGTTGCT
genomic: CTGGCTTCTCAGCTCAAGTTTATGAGCTATCTTCACACTTTCTTCATAAGgtaggacctt ... aaaaacacagGAGTGGATCATGGAACAATGGGATAAAAGTTTCTACATCAGTTCTGTTGCT
EST: gi|31359524|gb|CD443881.1|CD443881
EST:     CTGGCTTCTCAGCTCAAGTTTATGAGCTATCTTCACACTTTCTTCATAAG                         GAGTGGATCATGGAACAATGGGATAAAAGTTTCTACATCAGTTCTGTTGCT
genomic: CTGGCTTCTCAGCTCAAGTTTATGAGCTATCTTCACACTTTCTTCATAAGgtaggacctt ... aaaaacacagGAGTGGATCATGGAACAATGGGATAAAAGTTTCTACATCAGTTCTGTTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttcattctcttttgatgttctcaattttgcaaaaaacaaaaacaaaaacacagGAGTGGATCATGGAACAATGGGATAAAAGTTTCTACATCAGTTCTGTTGCTGGCTCCAACAATGGAAGTTCTATTGTAGTGATGTCAAAAG
           ttttgat  putative branch site (score: 4)
                                aaaaaacaaaaacaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggaccttcccatctgcacctcatgttcattctcttttgatgttctcaattttgcaaaaaacaaaaacaaaaacacagGAGTGGATCATGGAACAATGGGATAAAAGTTTCTACATCAGTTCTGTTGCTGGCTCCAACAATGGAAGTTCTATTGTAGTGATGTCAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG