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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gccttccatctcttaaagagttcataaacttttcataagataggacacacgattttcctttgctctgaataatttagctgttcttgttttccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGATTTACAAGGAAACCACCAAAGTATGAGCGGTTCATTCGACCAACTGGTCT

Basic information

species Zea mays
transcript GRMZM2G174204_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174204_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os07g47580.1 (Oryza sativa), 3'ss of exon 6
gccttccatctcttaaagagttcataaacttttcataagataggacacacgattttcc-tttgctctgaataatttagctgttcttg-----ttttccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGATTTACAAGGAAACCACCAAAGTATGAGCGGTTCATTCGACCAACTGGTCT
        |||   ||||   |  || |  |    ||  |  |  |  |  |  | || | || | | |   || |   |  |  |      |    | | | ||||||| ||||||||||||||||| || || ||||| ||||||||| |||| |||||||||||||||||||||||||| ||||| ||| | |||||||| ||
------tttctgccaaagcagttttacatgtcatctagtagtgatctgagaaactaccatgtgttattaggcatctgatttctgctaacgaatgacgcttatgcagCCAAACAGTGGAAGAGAATGGTCACTAAGGCCACCTTTGTTGGACCTGGGTTTACAAGGAAACCACCAAAGTATGAACGGTTTATTAGGCCAACTGGCCT

upper sequence: GRMZM2G174204_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA02G35500.1 (Glycine max), 3'ss of exon 6
gccttccatctcttaaagagttcataaacttttca-taagataggacacacgattttcctt--tgctctga--ataatttagctgttcttgttttccc--tgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGATTTACAAGGAAACCACCAAAGTATGAGCGGTTCATTCGACCAACTGGTCT
        | ||| |   |   ||  ||||  | | | |    || |    ||||||  |   || |||||  ||  | ||   ||   ||  |  ||  | | |||||||||| |||||||| |||||||| ||||| || ||||||||  |||| ||||| || ||||| |||||||| |||||||||||||| || || ||  |
-------gtgtctaattcaaaacaccaactcctaaatcatggtggtcttgtgattttattacatgatctgataattttctaatagtatatggctcaccatttttcagCCAAGCAATGGAAGAGGATGGTTACAAAAGCTACATTTGTTGGGCCTGGTTTTACCAGAAAACCTCCAAAGTACGAGCGGTTCATTCGTCCGACAGGATT

upper sequence: GRMZM2G174204_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA10G10000.1 (Glycine max), 3'ss of exon 6
gccttccatctcttaaag--agttcataaacttttcataagataggacacacgattttcctttgctctga--ataatttagctgt-tcttgttttcc-ctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGATTTACAAGGAAACCACCAAAGTATGAGCGGTTCATTCGACCAACTGGTCT
    || |  ||  ||    |  || |||| |  |  |    | |   |    |||    | |  |||||  ||  | ||   || | ||| |  ||  | | |||||||||| |||||||| |||||||| ||||| || ||||||||  |||| ||||| || || || |||||||||||||| |||||||| || || ||  |
----tctaattcaaaacaccaactcttaaa-tcatggtggtcttgtg-atttcattacattattatctgatgattttctaatagtatgttgctaaccatttttcagCCAAGCAATGGAAGAGGATGGTTACAAAAGCTACATTTGTTGGGCCTGGTTTTACCAGAAAGCCTCCAAAGTATGAGCGATTCATTCGTCCTACAGGATT

upper sequence: GRMZM2G174204_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv08s0105g00280.t01 (Vitis vinifera), 3'ss of exon 6
gccttccatctcttaaagagttcataaacttttcataagataggacacacgattt-tcctttgctctgaataatttagctgttcttgttttccctgt-----acagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGATTTACAAGGAAACCACCAAAGTATGAGCGGTTCATTCGACCAACTGGTCT
   ||  ||   | |    || |||| |   |  | | | |  | ||||       ||| || |          ||| |  |   ||| |  | |||      ||||||||||||||||||| ||||| ||||| ||||| || || ||| | |  |||||||| ||||| || ||||||||||| ||||| || ||  | ||  |
---ttagat---tgagcatgtgcatatatgctgaaaaggttgagtcacaaacccaatcccttacctaatgcctcttaacaatctatgtctggcatgtcttttgcagCCAAGCAGTGGAAGAGGATGGTAACCAAGGCCACGTTCGTGGGACCAGCTTTTACAAGAAAACCCCCCAAGTATGAGCGATTCATCCGTCCTTCGGGATT

upper sequence: GRMZM2G174204_T01 (Zea mays), 3'ss of exon 6
lower sequence: EFJ15002 (Selaginella moellendorffii), 3'ss of exon 6
gccttccatctcttaaagagttcataaacttttcataagataggacacacgattttcctttgctctgaataatttagctgttcttgttttccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGATTTACAAGGAAACCACCAAAGTATGAGCGGTTCATTCGACCAACTGGTCT
                           ||| ||       |    |||    |      | | |    ||  |||   | |||  || ||     | |||| || ||||||||| |||||||||| |||||||| ||||||||||| || || || ||||||||||||||||| ||| |||| ||  |||| |  ||  |
-------------------------gtactgttttctttgtctttcactttttaccggatggtttctcattgttt---tcttcgcgtcttggtgctccagCTAAACAGTGGAAGCGAATGGTTACTAAAGCCACATTTGTTGGAGCCGGTTTCACGAGGAAACCACCAAAGTACGAGAGGTTTATCAGACCCATGGGGTT

upper sequence: GRMZM2G174204_T01 (Zea mays), 3'ss of exon 6
lower sequence: EFJ37687 (Selaginella moellendorffii), 3'ss of exon 6
gccttccatctcttaaagagttcataaacttttcataagataggacacacgattttcc--tttgctctgaataatttagctgttcttgttttccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGATTTACAAGGAAACCACCAAAGTATGAGCGGTTCATTCGACCAACTGGTCT
                                       |  |    |    | || |  ||| | | | ||  |||  |  || || | ||| |  |  ||| || ||||||||| |||||||||| |||||||| ||||||||||| || || || ||||||||||| ||||| ||| |||| ||  | || |  ||  |
-------------------------------------gtactgttttctttgtctttcatttttcaccggatggtttctc-attgttttcttcgcgttttagCTAAACAGTGGAAGCGAATGGTTACTAAAGCCACATTTGTTGGAGCCGGTTTCACGAGGAAACCACCGAAGTACGAGAGGTTTATCAGGCCCATGGGGTT

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|60340980|gb|DN207953.1|DN207953
EST:     TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
genomic: TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAAgtaagtgact ... ccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
EST: gi|60354693|gb|DN221666.1|DN221666
EST:     TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
genomic: TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAAgtaagtgact ... ccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
EST: gi|60347312|gb|DN214285.1|DN214285
EST:     TGTTGTTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
genomic: TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAAgtaagtgact ... ccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
EST: gi|50332540|gb|CO527666.1|CO527666
EST:     TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
genomic: TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAAgtaagtgact ... ccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
EST: gi|45847152|gb|CN071095.1|CN071095
EST:     TGTAGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
genomic: TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAAgtaagtgact ... ccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
EST: gi|211523708|gb|FL481391.1|FL481391
EST:     CTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
genomic: CTACGAACTGGCAAGCGAAAAAgtaagtgact ... ccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
EST: gi|60350420|gb|DN217393.1|DN217393
EST:     TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
genomic: TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAAgtaagtgact ... ccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
EST: gi|211296298|gb|FL480002.1|FL480002
EST:     TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
genomic: TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAAgtaagtgact ... ccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
EST: gi|78109119|gb|DV527536.1|DV527536
EST:     TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
genomic: TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAAgtaagtgact ... ccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
EST: gi|5739867|gb|AI947557.1|AI947557
EST:     GGCAAGCGAAAAC                         CCAACCAGTGGAAGAGAATGGTTNCCAAAGCCNCTTTTGTTGGAGCTGGAT
genomic: GGCAAGCGAAAAAgtaagtgact ... ccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
EST: gi|60353886|gb|DN220859.1|DN220859
EST:     TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
genomic: TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAAgtaagtgact ... ccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
EST: gi|17930472|gb|BM267432.1|BM267432
EST:     TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
genomic: TGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAAgtaagtgact ... ccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
EST: gi|45847376|gb|CN071319.1|CN071319
EST:     GCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCCAGCGAAAAA                         CCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT
genomic: GCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAAgtaagtgact ... ccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGAT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 156

GTCAGACCTGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAAgtaagtgact ... ccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGATTTACAAGGAAACCACCAAAGTATGAGCGGTTCATTCGACCAACTGGTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 114

GTCAGACCTGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAAgtaagtgact ... ccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGATTTACAAGGAAACCACCAAAGTATGAGCGGTTCATTCGACCAACTGGTCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 131

GTCAGACCTGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAAgtaagtgact ... ccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGATTTACAAGGAAACCACCAAAGTATGAGCGGTTCATTCGACCAACTGGTCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 87

GTCAGACCTGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAAgtaagtgact ... ccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGATTTACAAGGAAACCACCAAAGTATGAGCGGTTCATTCGACCAACTGGTCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacacgattttcctttgctctgaataatttagctgttcttgttttccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGATTTACAAGGAAACCACCAAAGTATGAGCGGTTCATTCGACCAACTGGTCT
                                ctgttcttgttttccc  CT-rich tract
                    tgaataattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gccttccatctcttaaagagttcataaacttttcataagataggacacacgattttcctttgctctgaataatttagctgttcttgttttccctgtacagCCAAGCAGTGGAAGAGAATGGTTACCAAAGCCACTTTTGTTGGAGCTGGATTTACAAGGAAACCACCAAAGTATGAGCGGTTCATTCGACCAACTGGTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - ggacaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctgttc