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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGATAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATGgtaaataactagttagacatgcatgcttaagacattttaagtcctccctttcagatgatcctgaaagttatgcatcctggattagacaatgataaataaa...

Basic information

species Zea mays
transcript GRMZM2G044027_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044027_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g16980.4 (Oryza sativa), 5'ss of exon 4
GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGATAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATGgta--aataactagttag-acatgca-tgcttaagacatt-ttaagtcctccctttcagatgatcctgaaagttatgcatcctggattagacaatgataaataaa
|||||||| || || ||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||| ||||| |||||||    ||  |  | ||  |||  | | | | |   ||| |||  | ||     | |  |  | |||  ||  | |  |  | | | | |   ||| |||    
GTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATGgtattgctacattctcagtgcatttagttcatgaactattgttacatactagtaataaagttttactgctagcaa-gttttttcgttcaaaatttgagaaa----

upper sequence: GRMZM2G044027_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA12G06990.1 (Glycine max), 5'ss of exon 4
GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGATAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATGgtaaataactagttagacatgcatgcttaagacattttaagt-cctccctttcagatgatcctgaaagttatgcatcctggattagacaatgataaataaa---
|||||||||||||||||||  |||||||| ||||| || ||||| || || ||||| || || |||||||| ||||| || || ||||||| |  || | ||   | | | |  | ||  | | | || |  ||     | | ||  |   | |  | ||  |     | |||||  ||  |   |      
GTCATTGTTGCTGATAACTACTTCACTGGATCAAAGGACAACCTCAAAAAATGGATTGGTCATCCAAGATTCGAGCTTATTCGTCATGgtatactac-attttttcgtac-tattcaa--cgtgtcaactatctataaattaaattgttgggcatatgatagagtgaaggttagattatattttgtctcatt

upper sequence: GRMZM2G044027_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA13G40960.1 (Glycine max), 5'ss of exon 5
GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGATAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATGgtaaa---taac--tagttagacatgcatgcttaagacattttaagtcctccctttcag--atgatcctgaaagttatgcatcctggattagacaatgataaataaa
|| ||||||||||| ||||  |||||||| || || || ||||| || || ||||| || || |||||||||||||| ||||| ||||||| |   |||   | |||    ||  |   | ||     || || |  || | ||  |   |    |    || | |  |   | | ||    | || |       
GTAATTGTTGCTGACAACTACTTCACTGGATCCAAGGACAACCTCAAAAAATGGATAGGTCATCCAAGATTTGAGCTTATCCGTCATGgtatagtctaatctttgtttactatcaactatcaaaggcattaaaattgtcacattaggcagtatctccttgagcttttaaatttagtttgtcaactggt-------

upper sequence: GRMZM2G044027_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA12G06980.2 (Glycine max), 5'ss of exon 3
GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGATAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATGgtaaataactagttagacatgcatgcttaagacattttaagtcctccctt--tcagatgatcctgaaagttatgcatcctggattagacaatgataaataaa--
|||||||||||||| ||||| |||||||| || ||||| ||||| || || ||||| || || |||||||| ||||| || || |||||||  ||| |     |   |      |  |  ||||   || |     ||  |  |||| |    |   | |    | ||  || || ||   ||  | |    
GTCATTGTTGCTGACAACTTCTTCACTGGATCTAAAGACAACCTTAAAAAATGGATTGGCCATCCAAGATTCGAGCTAATTCGTCATGgta--taattttactgttctcttcattgcaatcattcacagactgggattaatttgatggttt--attctcaattgttctaaatcagtcaccaatgtagagcag

upper sequence: GRMZM2G044027_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA11G15010.1 (Glycine max), 5'ss of exon 4
GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGATAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATGgtaaataactagttagacatgcatgcttaagacattttaagtcctccctt--tcagatgatcctgaaagttatgcatcctggattagacaatgataaataaa--
|||||||||||||| ||||  |||||||| || ||||| ||||| || |  ||||| || || |||||||||||||| || || |||||||  ||| |         |      |  |  ||||   |||      ||  |  |||| |    |   | |    | ||  || ||  |   ||  | |    
GTCATTGTTGCTGACAACTACTTCACTGGATCTAAAGACAACCTTAAAAGATGGATTGGCCATCCAAGATTTGAGCTAATTCGTCATGgta--taattttactattctcttcattgcaatcattcacagtttgggattaatttgatggttt--attctcaattgttctaaatcagttaccaatgtagagcag

upper sequence: GRMZM2G044027_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA11G15020.1 (Glycine max), 5'ss of exon 4
GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGATAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATGgtaaataactagttagacatgcatgcttaagacattttaagt-cctccctttcagatgatcctgaaagttatgcatcctggattagacaatgataaataaa----
|||||||||||||| ||||  |||||||| ||||| || ||||| || || ||||| || || |||||||||||||| ||||| |||||||  ||     ||     | | |  | ||  | | | ||    ||     | | || ||  || |  | ||  |     |||||||  ||  |   |       
GTCATTGTTGCTGACAACTACTTCACTGGATCAAAGGACAACCTCAAAAAATGGATTGGTCATCCAAGATTTGAGCTTATCCGTCATGgta--tactccattttgtttac-tattcaa--cttctcaaccatctaaaaattaaattattgtgcatatgatagactgaagattagattatattttgtctcattt

upper sequence: GRMZM2G044027_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA15G04500.2 (Glycine max), 5'ss of exon 5
GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGATAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATGgtaaataactagttagacatgcatgcttaagacattttaagtcc--tccctttcagatgatcctgaaagttatgcatcctggattagacaatgataaataaa-
|||||||||||||| ||||  |||||||| || || |||||||| || |||||||| || || |||||||||||||| ||||| |||||||  ||     | |    ||  | ||    ||  |  |    |  | || || | ||  ||         ||||| |     ||    | ||||  ||    
GTCATTGTTGCTGACAACTACTTCACTGGATCCAAGGATAACCTCAAAAAGTGGATTGGTCATCCAAGATTTGAGCTTATCCGTCATGgta--tagtctttcatctttgtttactgtcaactatcaactatcaatgccattaaaattgtcacatgttagatgca-ctaaagttttttattgatttatcttt

upper sequence: GRMZM2G044027_T02 (Zea mays), 5'ss of exon 4
lower sequence: AT5G59290.2 (Arabidopsis thaliana), 5'ss of exon 3
GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGATAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATGgta-aataactagttagaca-tgcatgcttaag-acattttaagtcctccctttcagatgatcctgaaagttatgcatcctggattagacaatgataaataaa
||  ||||||||||||||| ||||||||| |||||||| ||||| |||||||||||||| ||||| || ||||| || || || || ||||   |  | ||     || |   |  |||||    || |   || |  |    ||||    |     | | |  ||   | ||| |       |||| |  
GTGGTTGTTGCTGATAACTATTTCACTGGCTCAAAAGAAAACCTCAAGAAGTGGATCGGTCACCCCAGGTTTGAACTTATTCGTCACGgtatggtctcgagactctcagtttgttgttaagcgtcttcttgttcatgtcaacaagatccatcatcgtgatctctatttggaatttgg--gctttaaacag-

upper sequence: GRMZM2G044027_T02 (Zea mays), 5'ss of exon 4
lower sequence: AT3G46440.1 (Arabidopsis thaliana), 5'ss of exon 4
GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGATAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATGgta-aataactagttagacatgcatgcttaagacattttaagt----cctccctttcagatgatcctgaaagttatgcatcctggattagacaatgataaataaa
|| |||||||||||||||| ||||||||||||||| || ||||| ||||||||||| || || |||||||||||||| ||||| || ||||   |    |  |   |  || || |   |  |||   | |      | ||| ||   || ||     | ||||  ||  ||| || |    | | |      
GTGATTGTTGCTGATAACTATTTCACTGGTTCAAAGGACAACCTTAAGAAGTGGATTGGTCATCCAAGATTTGAGCTTATCCGTCACGgtatggttttgaaattctctggcttgttgctgctattgagaatggaatattcctgtcttttgttctatccatttat--attttggttttgggtttaacag-----

upper sequence: GRMZM2G044027_T02 (Zea mays), 5'ss of exon 4
lower sequence: Vv06s0004g04390.t01 (Vitis vinifera), 5'ss of exon 4
GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGATAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATGgtaaataactagt-tagacatgcatgcttaagacattttaagtcctccctttcagatgatcctgaaagttatgcatcc--tggattagacaatgataaataaa
|| |||||||| |||||||  ||||| ||||| || || || || ||||| ||||| || || |||||||||||||| || || |||||||| |   |  | |    |  |    |||    ||   |  | |           |  |   |||  |     ||||  |    |  |   ||||   |   
GTAATTGTTGCCGATAACTACTTCACCGGTTCTAAGGACAATCTCAAGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATGgtaagttttttatctttttactccattttattttatcacatatgcatatgcgtcatttgtttggaatttgggatatcccttcagatgaatcctgattggt---

upper sequence: GRMZM2G044027_T02 (Zea mays), 5'ss of exon 4
lower sequence: Vv13s0019g00840.t01 (Vitis vinifera), 5'ss of exon 4
GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGATAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATGgtaaataactagttagacatgcatgcttaagacattttaagtcctccctttcagatgatcctgaaagttatgcatcctggattagacaatgataaataaa
|| ||||||||||||||||  |||||||| || ||||||||||||| ||| ||||| || || |||||||||||||| || || |||||||     ||  || |   ||       |||        | ||    || | | | |    |    || | |     |   |     |  | |  ||   
GTGATTGTTGCTGATAACTACTTCACTGGATCTAAAGATAACCTGAGGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATGgtattattctcatttgctttgtcattacaaggtggacacaatcaggactgttaaacgcctttccttgtcaagttctttatttgctggatgggttcatgtc

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|6637013|gb|AW261285.1|AW261285
EST:     TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATG                         ATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
genomic: TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATGgtaaataact ... tctgttttagATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
EST: gi|149097834|gb|EE183762.2|EE183762
EST:     TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATG                         ATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
genomic: TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATGgtaaataact ... tctgttttagATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
EST: gi|14206834|gb|BG840512.1|BG840512
EST:     CGGACACCCAAGATTTGAGCTCATCCGCCATG                         ATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
genomic: CGGACACCCAAGATTTGAGCTCATCCGCCATGgtaaataact ... tctgttttagATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
EST: gi|6194647|gb|AW146751.1|AW146751
EST:     TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATG                         ATGTCACTGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
genomic: TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATGgtaaataact ... tctgttttagATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
EST: gi|6020952|gb|AW065880.1|AW065880
EST:     TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATG                         ATGTCACTGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
genomic: TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATGgtaaataact ... tctgttttagATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
EST: gi|211032180|gb|FL277400.1|FL277400
EST:     TCATCCGCCATG                         ATGTCACTGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
genomic: TCATCCGCCATGgtaaataact ... tctgttttagATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
EST: gi|60672298|gb|DN475062.1|DN475062
EST:     TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATG                         ATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGGTCTATCACCTTGCTT
genomic: TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATGgtaaataact ... tctgttttagATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
EST: gi|32788262|gb|CD940498.1|CD940498
EST:     TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATG                         ATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATC
genomic: TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATGgtaaataact ... tctgttttagATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATC
EST: gi|40334152|gb|CK368222.1|CK368222
EST:     TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATG                         ATGTCACCGAGCCACTTCTTGTGGAGTTTGACCAGATCTATCACCTTGCTT
genomic: TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATGgtaaataact ... tctgttttagATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
EST: gi|22473192|gb|BU037672.1|BU037672
EST:     TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATG                         ATGTCACTGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
genomic: TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATGgtaaataact ... tctgttttagATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
EST: gi|213173372|gb|FM186537.1|FM186537
EST:     TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATG                         ATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
genomic: TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATGgtaaataact ... tctgttttagATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
EST: gi|26558105|gb|CA830340.1|CA830340
EST:     TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATG                         ATGTCACTGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
genomic: TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATGgtaaataact ... tctgttttagATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
EST: gi|148945878|gb|EC891170.2|EC891170
EST:     TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATG                         ATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
genomic: TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATGgtaaataact ... tctgttttagATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
EST: gi|67016223|gb|CO444972.1|CO444972
EST:     TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATG                         ATGTCACTGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
genomic: TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATGgtaaataact ... tctgttttagATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
EST: gi|67013235|gb|CO441984.1|CO441984
EST:     TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATG                         ATGTCACTGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
genomic: TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATGgtaaataact ... tctgttttagATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
EST: gi|21987903|gb|BQ779431.1|BQ779431
EST:     TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATG                         ATGTCACTGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
genomic: TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATGgtaaataact ... tctgttttagATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
EST: gi|32165003|gb|CD670321.1|CD670321
EST:     TAACCTGAAGAAG-GGATCGGACACCCAAGATTTGAGCTCATCCGCCATG                         ATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
genomic: TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATGgtaaataact ... tctgttttagATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
EST: gi|148951041|gb|EC896695.2|EC896695
EST:     TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATG                         ATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT
genomic: TAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATGgtaaataact ... tctgttttagATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGATAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTCATCCGCCATGgtaaataactagttagacatgcatgcttaagacattttaagtcctccctttcagatgatcctgaaagttatgcatcctggattagacaatgataaataaa

- - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA