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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gggaagtaggcctatctttcatataattgaaaattgatttttttttctgaggcactaggtattagccaactctcacctcttgtgtatttctttcttttagATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATTCAGGTCAATGGTGGTACCATTGCTGACAAGGTGGACTACGGCTATAAAT

Basic information

species Zea mays
transcript GRMZM2G135727_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G135727_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os11g06750.1 (Oryza sativa), 3'ss of exon 4
-------------------------gggaagtaggcctatctttcatataattgaaaattgatttttttttctgaggcactaggtattagccaactctcacctcttgtgtatttctttcttttagATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATTCAGGTCAATGGTGGTACCATTGCTGACAAGGTGGACTACGGCTATAAAT
                              |||     | |  |  |||    |  |||||  |  |     || |     |  | || |   | |||||  |  |   | ||| | |  || |||||||||| |||||||| ||||||||||||||||||||||| |||||||| ||| ||||||||||||||||||| || ||||||||||| || || || |
gtcagtaacctactgttattttactatcttgtattttgagcccttctatt-cagttaattggatggtaaccatgtgctgtaaattgtttgttcattctca--ttctaaatctttatgtgcttcagATTAGGAAAATGAAGGGCTTGAAGCAGAAGAAGGCTCACCTCATGGAGATCCAGATCAATGGTGGTACCATTGCCGATAAGGTGGACTATGGATACAAGT

upper sequence: GRMZM2G135727_T03 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA20G30810.1 (Glycine max), 3'ss of exon 4
gggaagtaggcctatctttcatataattgaaaattgatttttttttctgaggcactaggtattagccaactctcacctcttgtgtatttctt---tcttttagATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATTCAGGTCAATGGTGGTACCATTGCTGACAAGGTGGACTACGGCTATAAAT
      |     |    ||  |  ||||  ||||| |   |  || | |       | |  ||||  |  |  |   |    ||| |  |||   ||||  |||| ||||| ||||| || |||||||||||||| || ||  | ||||| |||||||| ||||||||||| |||||  | ||||||||||  |  || |  |
---ccttctattttgtgtttgtcaaattccaaattcagagtccttccagttatcacatgatttagatatattcctaatagcctgtctggcttaaatcttacagATCAGGAAAATGAAAGGGTTGAAGCAGAAGAAAGCCCATATCATGGAAATTCAGGTTAATGGTGGTACTATTGCACAGAAGGTGGACTTTGCATACAGTT

upper sequence: GRMZM2G135727_T03 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA10G36780.1 (Glycine max), 3'ss of exon 4
gggaagtaggcctatctttcatataattgaaaattgatttt--tttttctgaggcactaggtattagccaactctcacctcttgtgtatttctt---tcttttagATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATTCAGGTCAATGGTGGTACCATTGCTGACAAGGTGGACTACGGCTATAAAT
      || |    | |       |||| | | |   ||    || |    |   |  | |  | ||     |  |   |  | ||| |  |||   ||||  |||| ||||| ||||| || |||||||||||||| || ||  | ||||| |||||||| ||||||||||  |||||  | ||||||||||  |  || |  |
-----ttatgttcttttaattccaaattaagagtcacttccaattatcacaaattatcatgattgagatttattcctaatagtctgtctgccttgaatcttacagATCAGGAAAATGAAAGGGTTGAAGCAGAAGAAAGCCCATATCATGGAAATTCAGGTTAATGGTGGTAGTATTGCACAAAAGGTGGACTTTGCATACAGTT

upper sequence: GRMZM2G135727_T03 (Zea mays), 3'ss of exon 4
lower sequence: AT1G43170.7 (Arabidopsis thaliana), 3'ss of exon 4
gggaagtaggcctatctttcatataattgaaaattgatttttttttctgaggcactaggtattagccaactctcacctcttgtgtatttctttcttttagATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATTCAGGTCAATGGTGGTACCATTGCTGACAAGGTGGACTACGGCTATAAAT
 | ||||  || |||  |  ||  || || | ||  ||    | |||||   ||||| ||  |  |  ||       |  | |||      |  ||  |||| |||||||||||||| ||||||||||||||||||||| |||||||||| ||| |||||||||||||||||||  | ||||| ||||  | ||| |  |
-gtaagtttgcttat--tgaatggaagtgtatatc-ataaactcttctg---cactacgttcttactgac-----aattctatgtgacctctaattacagATCAGGAAGATGAAGGGATTGAAGCAGAAGAAGGCTCACATGATGGAGATCCAGATCAATGGTGGTACCATTGCCCAGAAGGTTGACTTTGCCTACAGTT

upper sequence: GRMZM2G135727_T03 (Zea mays), 3'ss of exon 4
lower sequence: AT1G61580.1 (Arabidopsis thaliana), 3'ss of exon 4
gggaagtaggcctatctttcatataattgaaaattgatttttttttctgaggcactaggtattagccaactctcacctcttgtgtatttctttcttttagATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATTCAGGTCAATGGTGGTACCATTGCTGACAAGGTGGACTACGGCTATAAAT
              | |  ||| || || ||| || |   |  |||   |      |  | ||   |   |  |   | |||  |||       |||||||| ||||| ||||| ||  |||||||||||||||| || ||||  ||||||||| ||||||||||    || ||  | || || ||||| | ||  |  |
-------------gtatgccatttacttcaaa-ttcacaatcattttgcaaatttcatttgtt--tctgattacgattgttggatat------gttttagATAAGGAAAATGAAAGGGCTGAAGCAGAAGAAGGCACATCTGAATGAGATTCAGATCAATGGTGGAGATATAGCAAAGAAAGTTGACTATGCCTGCAGTT

upper sequence: GRMZM2G135727_T03 (Zea mays), 3'ss of exon 4
lower sequence: Vv18s0072g00340.t01 (Vitis vinifera), 3'ss of exon 4
gggaagtaggcctatctttcatataattgaaaattgatttttttttctgagg--cactaggtattagccaactctcacct--cttgtgtatttctt-tcttttagATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATTCAGGTCAATGGTGGTACCATTGCTGACAAGGTGGACTACGGCTATAAAT
      ||       |||    ||| || |||||| | ||     ||| |    | |||  |  |    | |    | ||   || | |  |  |  | || |||||||||||||||||||| |||||||||||||| || ||| |||||||||| |||||||||||||| ||||||||| | || ||||| || |  |||   |
-----ttatttgacgcttgtcaatacttcaaaatttagttccagctctcatatcccctaaatgatccttatcctctaactaatttctctggtcatggtgttatagATTAGGAAGATGAAGGGATTGAAGCAGAAGAAAGCACACTTGATGGAGATCCAGGTCAATGGTGGAACCATTGCTCAGAAAGTGGATTATGCTTATGGTT

upper sequence: GRMZM2G135727_T03 (Zea mays), 3'ss of exon 4
lower sequence: Vv12s0035g01020.t01 (Vitis vinifera), 3'ss of exon 3
----------gggaagtaggcctatctttcatataattgaaaattgatttttttttctg--aggcactaggtattagccaactctcacctcttgtgtatttctttcttttagATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATTCAGGTCAATGGTGGTACCATTGCTGACAAGGTGGACTACGGCTATAAAT
             |   |    |    |||| | | || |   || |  ||| |   ||  ||  || |  |||| | || ||  ||  || | | |         || |||||||| || ||||||||  |||||||||| ||||||||||| |||||||||||||| ||||||||     ||||| | ||||| ||||| | ||||   |
gtagttttccatcaccaatatttgggattcaaagactttaggtttcacatttataaatgcaagttaccaattatttggca-ctgacatatcctatatggaatggatttgtagATTAGAAAAATGAAGGGCCTGAAGCAGAAAAAGGCTCACCTTATGGAGATTCAGGTGAATGGTGGAGATGTTGCTAAGAAGGTTGACTATGCCTATGGTT

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|67020267|gb|CO449016.1|CO449016
EST:     AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAG                         ATTAGGAAGATGAAGGGTTTGAAGCANAAGAAGGCTCACCTGATGGAGATT
genomic: AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagct ... tttcttttagATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT
EST: gi|67024182|gb|CO452931.1|CO452931
EST:     AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAG                         ATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT
genomic: AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagct ... tttcttttagATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT
EST: gi|211054045|gb|FL387661.1|FL387661
EST:     AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAG                         ATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT
genomic: AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagct ... tttcttttagATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT
EST: gi|78122260|gb|DV540644.1|DV540644
EST:     AGAAGATGAAAAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAG                         ATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT
genomic: AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagct ... tttcttttagATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT
EST: gi|211286419|gb|FL307760.1|FL307760
EST:     AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAG                         ATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT
genomic: AGAAGATGAAGAAATATGCTTCTGTTATCCGTGTCATTGCTCATACCCAGgtaagaagct ... tttcttttagATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgaggcactaggtattagccaactctcacctcttgtgtatttctttcttttagATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATTCAGGTCAATGGTGGTACCATTGCTGACAAGGTGGACTACGGCTATAAAT
                        ctctcac  putative branch site (score: 3)
                        ctctcacctcttgtgt  CT-rich tract
                                       tatttctttctttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gggaagtaggcctatctttcatataattgaaaattgatttttttttctgaggcactaggtattagccaactctcacctcttgtgtatttctttcttttagATTAGGAAGATGAAGGGTTTGAAGCAGAAGAAGGCTCACCTGATGGAGATTCAGGTCAATGGTGGTACCATTGCTGACAAGGTGGACTACGGCTATAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - -ttcatat
- - - - - - - - - - - - - - - - - - - - - ttttctg
- - - - - - - - - - - - - - - - - - - - - - - - - -gcactag