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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatctattgtgttcagtgaaaagcttttcctagttcagcctgatttggtgtcattttatgactgcgtggatcatgtgttcagGACTTGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACG

Basic information

species Zea mays
transcript GRMZM2G179308_T04
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G179308_T03 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os12g27520.1 (Oryza sativa), 3'ss of exon 8
gtatctattgtgttcagtgaaaagcttttcctagttcagcctgatt-tggtgtcattttatgactgcg-tggatcatg---tgttcagGACTTGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACG
|||| | |  ||   |||| ||||| || |||   ||||| ||||| |||| |   |||| || ||   ||| |  ||   |||||||||||||||||||||||||| |||||||| ||||||||||||||||| || |||||||| ||||||
gtatttgtcttgcctagtgcaaagccttccctg--tcagcgtgattatggtttatgtttacgattggaatggctgttgttctgttcagGACTTGGATGGAGTTACCCCTGTGATATATGGAGTGTTGGTTGTATACTGGTTGAGCTATGCACG

upper sequence: GRMZM2G179308_T03 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA17G13440.2 (Glycine max), 3'ss of exon 7
-------------------------------------gtatcta-ttgtgttcagtgaaaag-cttttcctagt--tcagcctgatttggtgtcatttta---tgactgcgtggatcatgtgttcagGACTTGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACG
                                      | ||||  ||||||  |      | |   |   | |  | ||   |  |   ||  |  | |   ||| |  |   || |||| || ||||||||| ||||| || |||||||||||||||||||| || |||||  | |||||| | ||||||
gtatatatacatactgtaaatgctgtggaaagaatgcctgtctaactgtgttttgcatgttgacacatgacaatcatgagaagggctatatgcaagctaaagttgattttggcaatgatgt-tttagGACTTGGCTGGAGCTATCCATGTGATATCTGGAGTGTGGGATGTATCTTGGTTGAGTTATGCACG

upper sequence: GRMZM2G179308_T03 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA06G18530.1 (Glycine max), 3'ss of exon 7
------------------------------gtatcta-ttgtgttca-gtgaaaagcttttcctagttcagcctgatt-tggtgtcattttatgact--gcgtggatcatgtgttc--agGACTTGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACG
                              || | || ||| || ||  ||      |  | | |   ||   || || || || ||  | |  |||     | |   |||  ||   ||||||||| ||||| || ||||||||||| |||||||| |||||||| || |||||  | ||||| 
gtacataaatattcagtaaaaatgctacgagtttttaattgggtacatatgctgttatacttccaaaacatggtgtttatgatgccaactgaatacttgatattggcaatggttttgtagGACTTGGGTGGAGCTATCCATGTGATATATGGAGTGTGGGTTGTATACTGGTTGAATTATGCACT

upper sequence: GRMZM2G179308_T03 (Zea mays), 3'ss of exon 7
lower sequence: Vv17s0000g09500.t01 (Vitis vinifera), 3'ss of exon 8
---------------------------------------------------------------------gtatctattgtgttcagtgaaaagcttttcctagttc-----------agcctgatttggtgtcatttt-atgactgcg---tggatcatgt--gttcagGACTTGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACG
                                                                       ||   ||| |     | | | | || |  || | |           |    ||| | ||  | |  | |||| | ||   |   ||||||   |  ||| |||||||||||||| ||||||||||| ||||||||||| |||||  | || ||| | ||||||
gtatgccatcaaatatctgccattgtttttctgttgtcatgagtcagtatggtgttctaccattctttcaaattagttg-gccagatcacaggtttcttttaatgcccaaggaagacaagtggatatagttccttgctgatgaatacgctttttttcatgtttatgtagGGCTTGGATGGAGTTATCCATGTGATATATGGAGTGTTGGATGTATCTTGGTGGAGTTATGCACG

upper sequence: GRMZM2G179308_T03 (Zea mays), 3'ss of exon 7
lower sequence: Vv01s0137g00580.t01 (Vitis vinifera), 3'ss of exon 8
gtatctattgtgttcagtgaaaagcttttcctagttcagcctgatttggtgtcattttatgactgcgtgg----atcatgtgt-----tcagGACTTGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACG
           ||    | | | | |  |    |||     ||| ||| |  ||||| |    | |   |    ||||| | |     ||||| |||||||||||||| |||||||| || ||||| |||||||||||  | || || || ||  ||
-----------gtgtgtttatatgttcctttctgttatcattgacttgcttacatttcagcggtcctcagtgtcatcatatttgtttttcagGGCTTGGATGGAGTTATCCATGTGACATGTGGAGCGTTGGTTGTATATTGGTGGAACTATGTTCG

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|32787565|gb|CD936467.1|CD936467
EST:     GAGTTATATTGTGTCGACGAGGCATTATCGGGCTCCAGAAGTTATACTGG                         AACTTGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTG
genomic: GAGTTATGTTGTGTCGACGAGGCATTATCGGGCTCCAGAAGTTATACTGGgtatctattg ... atgtgttcagGACTTGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTG
EST: gi|76015336|gb|DT942506.1|DT942506
EST:     GAGTTATGTTGTGTCGACGAGGCATTATCGGGCTCCAGAAGTTATACTGG                         GACTTGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTG
genomic: GAGTTATGTTGTGTCGACGAGGCATTATCGGGCTCCAGAAGTTATACTGGgtatctattg ... atgtgttcagGACTTGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTG
EST: gi|71756384|gb|DR954321.1|DR954321
EST:     GAGTTATGTTGTGTCGACGAGGCATTATCGGGCTCCAGAAGTTATACTGG                         GACTTGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTG
genomic: GAGTTATGTTGTGTCGACGAGGCATTATCGGGCTCCAGAAGTTATACTGGgtatctattg ... atgtgttcagGACTTGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTG
EST: gi|32850031|gb|CD989712.1|CD989712
EST:     GAGTTATGTTGTGTCAACGAGGCATTATCGGGCTCCAGAAGTTATACTGG                         GACTTGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTG
genomic: GAGTTATGTTGTGTCGACGAGGCATTATCGGGCTCCAGAAGTTATACTGGgtatctattg ... atgtgttcagGACTTGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTG
EST: gi|60357877|gb|DN224850.1|DN224850
EST:     GAGTTATGTTGTGTCGACGAGGCATTATCGGGCTCCAGAAGTTATACTGG                         GACTTGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTG
genomic: GAGTTATGTTGTGTCGACGAGGCATTATCGGGCTCCAGAAGTTATACTGGgtatctattg ... atgtgttcagGACTTGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTG
EST: gi|32934327|gb|CF039139.1|CF039139
EST:     GAGTTATGTTGTGTCGACGAGGCATTATCGGGCTCCAGAAGTTATACTGG                         GACTTGGGTGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTG
genomic: GAGTTATGTTGTGTCGACGAGGCATTATCGGGCTCCAGAAGTTATACTGGgtatctattg ... atgtgttcagGACTTGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTG
EST: gi|60347445|gb|DN214418.1|DN214418
EST:     GAGTTATGTTGTGTCGACGAGGCATTATCGGGCTCCAGAAGTTATACTGG                         GACTTGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTG
genomic: GAGTTATGTTGTGTCGACGAGGCATTATCGGGCTCCAGAAGTTATACTGGgtatctattg ... atgtgttcagGACTTGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTG
EST: gi|45568628|gb|CK986157.1|CK986157
EST:     GAGTTATGTTGTGTCGACGAGGCATTATCGAGCTCCAGAAGTTATACTGG                         GACTTGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTG
genomic: GAGTTATGTTGTGTCGACGAGGCATTATCGGGCTCCAGAAGTTATACTGGgtatctattg ... atgtgttcagGACTTGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctagttcagcctgatttggtgtcattttatgactgcgtggatcatgtgttcagGACTTGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACG
          gcctgat  putative branch site (score: 4)
                       tcattttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatctattgtgttcagtgaaaagcttttcctagttcagcctgatttggtgtcattttatgactgcgtggatcatgtgttcagGACTTGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT