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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaattttgtactcagctgtatgttttgagtgtttgattgttctatccagtcctaaggtggtgtgctttatggcaaaatagGTCTGGGATTACCAGACGAAGAGCTGTGTTCAGACACTTGAAGGGCATACACATAATATTTCTGCTGTTTGTTTCCATCCTGAGCTCCCTATAATCATTA

Basic information

species Zea mays
transcript GRMZM2G000645_T03
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G000645_T03 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 7
---gtacaattttgtactcagctgtatgttttgagtgtttgattgttctatccagtcctaaggtggtgtgctttatggcaaaatagGTCTGGGATTACCAGACGAAGAGCTGTGTTCAGACACTTGAAGGGCATACACATAATATTTCTGCTGTTTGTTTCCATCCTGAGCTCCCTATAATCATTA
    |    || | | | |   ||  ||||   ||| |   |   |||| | |||||||||| ||||||| |  ||||  ||  |||||||||||||||| ||||||||||||||||||||||||||||| |||||||| || ||||||||||||||||||||||||||||| |||||||||||||
gttttttttttctatccacttttgagtgttccaagtatcc-acgattctgtgcagtcctaagatggtgtggtc-atggtgaaccagGTCTGGGATTACCAAACGAAGAGCTGTGTTCAGACACTTGAAGGACATACACACAACATTTCTGCTGTTTGTTTCCATCCTGAGCTTCCTATAATCATTA

upper sequence: GRMZM2G000645_T03 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 7
-------------------------gtacaattttgtactcagctgtatgttttgagtgtttgattgttctatccagtcctaaggtgg-tgtgctttatggcaaaatagGTCTGGGATTACCAGACGAAGAGCTGTGTTCAGACACTTGAAGGGCATACACATAATATTTCTGCTGTTTGTTTCCATCCTGAGCTCCCTATAATCATTA
                          ||     |||||| ||  |  || |    |    |  ||   | |    ||   |||  ||| ||    |||||   ||  |||| |||||||| ||||| || || ||||| ||||| || ||||| || ||||| ||| | |||||||| || || |||||||| || |||||||||||||
gttttgttttcatttgttgcttgatctatctgcttgtacgcatttacatatacatacatatatatatatatgaaaaggaataacatggatgaaacttatg---aatcagGTATGGGATTATCAGACCAAAAGTTGTGTCCAGACCCTAGAAGGTCACACACACAATGTATCTGCTGTATGCTTTCATCCTGAACTTCCTATAATCATTA

upper sequence: GRMZM2G000645_T03 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 7
------gtacaattttgtactcag-ctgtatgttttgagtgtttgattgttc-tatccagtcctaaggtggtgtgcttta--------tggcaaaatagGTCTGGGATTACCAGACGAAGAGCTGTGTTCAGACACTTGAAGGGCATACACATAATATTTCTGCTGTTTGTTTCCATCCTGAGCTCCCTATAATCATTA
       |   ||||  | || |  || | || ||   | |          |  |  ||    | |   ||  |    |         |  | ||  |||| |||||||| ||||| || || ||||| ||||| || ||||| || ||||| ||| | |||||||| || || |||||||| || |||||||||||||
gttttgttttcatttgttgcttaatctatctgcttgtcgcgcacacgcacacacacacatgtatgaaaaggaataacatggatgaaacttacgaatcagGTATGGGATTATCAGACCAAAAGTTGTGTCCAGACCCTAGAAGGTCACACACACAATGTATCTGCTGTATGCTTTCATCCTGAACTTCCTATAATCATTA

upper sequence: GRMZM2G000645_T03 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 7
----------------gtacaattttgtactcagctgtatgttttgagtgtttgattgt---tctatccagtcctaaggtggtgtgctt-tatggc----aaaatagGTCTGGGATTACCAGACGAAGAGCTGTGTTCAGACACTTGAAGGGCATACACATAATATTTCTGCTGTTTGTTTCCATCCTGAGCTCCCTATAATCATTA
                 |    ||||   ||      |   |||    || |||  | |   | |||   |     |  |  | |||   ||   |     ||| |||| ||||| || || || || || ||||| ||||| || ||||| || ||||| ||| | ||||||||||| || |||||||| || |||||||||||||
gtttgttttctattttctgtttttttcctcttcatcttccctttaatttggttgcctatatgtgtatatggataggaattattatgccaataaaacctttgaaacagGTATGGGACTATCAAACCAAAAGTTGTGTCCAGACTCTAGAAGGTCACACACACAATGTATCTGCTGTTTGCTTTCATCCTGAACTACCTATAATCATTA

upper sequence: GRMZM2G000645_T03 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 7
----------------gtacaattttgtactcagctgtatgtt--ttgagtgtttgattgttctatccagtcctaaggtggtgtgctt-tatggc----aaaatagGTCTGGGATTACCAGACGAAGAGCTGTGTTCAGACACTTGAAGGGCATACACATAATATTTCTGCTGTTTGTTTCCATCCTGAGCTCCCTATAATCATTA
                 |    |||  |  ||| ||      |  ||  || |   ||  || |||   |     |  |  | |||   ||   |     ||  |||| |||||||| || || || || ||||| ||||| || ||||| || ||||| ||| | |||||||| || || |||||||| || |||||||||||||
gtttgttttctattttctgttttttcctcttcatcttccctctaatttggtttcctatatttgtatatggataggaattattatgccgataaaacctttgaatcagGTATGGGATTATCAAACCAAAAGTTGTGTCCAGACTCTAGAAGGTCACACACACAATGTATCTGCTGTATGCTTTCATCCTGAACTACCTATAATCATTA

upper sequence: GRMZM2G000645_T03 (Zea mays), 3'ss of exon 7
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 11
-------------------------------------------------gtacaattttgtact--cagctgtatgttttgagtgtttgattgttc-----tatccagtcctaaggtg---gtgtgctttatggcaaaatagGTCTGGGATTACCAGACGAAGAGCTGTGTTCAGACACTTGAAGGGCATACACATAATATTTCTGCTGTTTGTTTCCATCCTGAGCTCCCTATAATCATTA
                                                 || |   | ||||    ||  |||||  ||||  | |  | | || |     | ||   |  ||   ||    |    ||  |    ||  |||| ||||||||||| || ||||| || |||||||| || ||||| |||||||| ||| ||||||| || | ||| ||||| ||||| |||||||| ||||
gtctgtactgagctttcttgcttctttgcaagttgtttgctacatatgtgtgcttgtatgtatctccatttgtattgtttgtatataggttcgtgcagggttttctgtttgtatattgttcataaatttcttctggaagcagGTGTGGGATTACCAAACAAAGAGTTGCGTTCAGACTCTCGAAGGTCATACACACAATGTTTCTGCAGTATCTTTTCATCCAGAGCTACCTATAATTATTA

upper sequence: GRMZM2G000645_T03 (Zea mays), 3'ss of exon 7
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 7
gtaca-attttgtactca---gctgtatgttttgagtgtttgattgttctatccagt--cctaaggtggtgtgctttatggcaaaatagGTCTGGGATTACCAGACGAAGAGCTGTGTTCAGACACTTGAAGGGCATACACATAATATTTCTGCTGTTTGTTTCCATCCTGAGCTCCCTATAATCATTA
||    || |  | || |    ||  ||   ||   | | ||    ||| ||    |  | |   ||| | |   || |||   || |||| ||||| ||||| || || || |||||||||||||| ||||| || ||||| ||| ||||| | || ||||||||||| ||||| ||||| ||  |||
gtgtttatctgatgcttattgactaaatagcttccatttatgtgcattccatttgattactttctgtgat-taaattttggtggaacagGTGTGGGACTACCAAACCAAAAGTTGTGTTCAGACACTAGAAGGCCACACACACAATGTTTCTTCAGTCTGTTTCCATCCAGAGCTTCCTATTATTTTTA

upper sequence: GRMZM2G000645_T03 (Zea mays), 3'ss of exon 7
lower sequence: PP1S243_63V6.1 (Physcomitrella patens), 3'ss of exon 7
-------gtacaattttgtactcagctgtatgtt--ttgagtgtttga-ttgttc--tatccagtcctaaggtggtgtgctttatggc------aaaatagGTCTGGGATTACCAGACGAAGAGCTGTGTTCAGACACTTGAAGGGCATACACATAATATTTCTGCTGTTTGTTTCCATCCTGAGCTCCCTATAATCATTA
       ||| ||  |  |  | |  || |  |   |||    ||  | |||||   |||  | | || || |    | | |   |         |   |||| ||||||||||| || ||||||||||| |||||  | || || ||| | |||||| | ||||| || |||||||||||||||||||| || ||  | |
cgacgtggta-aacgtcatgtttaagtgaagatcacttggtcattcaagttgttgcatattgattgcttagtttcccttcctggcgttctctttgatgcagGTGTGGGATTACCAAACCAAGAGCTGTGTGCAGACTTTAGAGGGTCATTCTCATAATGTGTCTGCAGTGTGTTTCCATCCTGAGCTCCCCATCATTTTAA

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|26457397|gb|CA828980.1|CA828980
EST:     GTGG-GACAGGCCCTATTTGATTACTGGTTCTGATGACTCCACCGCAAAG                         GTCTGGGATTACCAGACGAAGAGCTGTGTTCAGACACTTGAAGGGCATACA
genomic: GTGGTGACAGGCCCTATTTGATTACTGGTTCTGATGACTCCACCGCAAAGgtacaatttt ... ggcaaaatagGTCTGGGATTACCAGACGAAGAGCTGTGTTCAGACACTTGAAGGGCATACA
EST: gi|32931674|gb|CF036486.1|CF036486
EST:     GTGGTGACAGGCCCTATTTGATTACTGGTTCTGATGACTCCACCGCAAAG                         GTCTGGGATTACCAGACGAAGAGCTGTGTTCAGACACTTGAAGGGCATACA
genomic: GTGGTGACAGGCCCTATTTGATTACTGGTTCTGATGACTCCACCGCAAAGgtacaatttt ... ggcaaaatagGTCTGGGATTACCAGACGAAGAGCTGTGTTCAGACACTTGAAGGGCATACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagtgtttgattgttctatccagtcctaaggtggtgtgctttatggcaaaatagGTCTGGGATTACCAGACGAAGAGCTGTGTTCAGACACTTGAAGGGCATACACATAATATTTCTGCTGTTTGTTTCCATCCTGAGCTCCCTATAATCATTA
     gtttgat  putative branch site (score: 5)
                                                aaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacaattttgtactcagctgtatgttttgagtgtttgattgttctatccagtcctaaggtggtgtgctttatggcaaaatagGTCTGGGATTACCAGACGAAGAGCTGTGTTCAGACACTTGAAGGGCATACACATAATATTTCTGCTGTTTGTTTCCATCCTGAGCTCCCTATAATCATTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT