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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCATCCTACTCCCACTAGGGCAGAAGTTTCTGACATAGCTATTGCAGTTCGGGAAGGTGCTGATGCCATCATGTTATCTGGCGAAACTGCTCATGGAAAgtaaggttcaacacttgttgctgtttaaatgtagtgttatcctaaacgctaaatggcaaaatagtcggtcacctgcagtttagccattatttgggttaaa...

Basic information

species Zea mays
transcript GRMZM2G033526_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G033526_T02 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os10g42100.1 (Oryza sativa), 5'ss of exon 8
ACCATCCTACTCCCACTAGGGCAGAAGTTTCTGACATAGCTATTGCAGTTCGGGAAGGTGCTGATGCCATCATGTTATCTGGCGAAACTGCTCATGGAAAgtaaggttcaacacttgttgctgtttaaatgtagtgttatcctaaacgctaaatggcaaaatagtcggtcacctgcagtttagccattatttgggttaaa--------------------------------------------------
||||||| ||||| || || |||||||||||||| ||||| ||||||||||| |||||| |||||||||||||| | ||||| |||||||| ||||||||||||| ||  | || ||   | | |||  | | || ||||  |   |  |      | ||  | |   |  | |  || |    |  |   ||  |  ||                                                  
ACCATCCCACTCCAACAAGAGCAGAAGTTTCTGATATAGCAATTGCAGTTCGTGAAGGTTCTGATGCCATCATGCTGTCTGGTGAAACTGCCCATGGAAAgtaagatttca-acctgacacaggttactttttgt-ttatgttcctccatgtgcatccaagaaatttatttctttaagctcttgctgtgggtgcatagaattctgctttccaattagacttaccttgattgtgcatcttactgtgtttag

upper sequence: GRMZM2G033526_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA01G40860.1 (Glycine max), 5'ss of exon 7
ACCATCCTACTCCCACTAGGGCAGAAGTTTCTGACATAGCTATTGCAGTTCGGGAAGGTGCTGATGCCATCATGTTATCTGGCGAAACTGCTCATGGAAAgtaaggttcaacacttgttgctgtttaaa--tgtagtgttatcctaaacgctaaatggcaaaatagtcggtcacc-tgcagtttagccattatttgggttaaa
| ||||| || || || |||||||||||||| ||||| || ||||||||  |  ||||||||||||| |||||| | || || |||||||| |||||||||| || ||      |  ||| ||   |    |    | || |  |      ||  ||   |||   |   |||   | || |||    | ||||||   |  |
ATCATCCCACACCAACAAGGGCAGAAGTTTCAGACATCGCAATTGCAGTAAGACAAGGTGCTGATGCTATCATGCTTTCAGGAGAAACTGCACATGGAAAgtgag-tttgctgttccttggtgaccatggttcctatattttatttttatttagctgttcaaactttttttcaatattcaattt--ttactatttgaaatgca

upper sequence: GRMZM2G033526_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA11G04490.1 (Glycine max), 5'ss of exon 4
ACCATCCTACTCCCACTAGGGCAGAAGTTTCTGACATAGCTATTGCAGTTCGGGAAGGTGCTGATGCCATCATGTTATCTGGCGAAACTGCTCATGGAAAgtaaggtt--caacacttgttgctgtttaaatgtagtgttatcctaaacgctaaatggcaaaatagtcggtcacctgcagtttagccattatttgggttaaa----
| ||||| || || |  ||||||||||| || ||||| || ||||||||  |  ||||||||||||| |||||| | || || |||||||| |||||||||| |  ||       |||| ||   |||     ||   ||    |      ||  ||   |||   |   |||       |||    | ||||||   |  |    
ATCATCCCACACCGAGGAGGGCAGAAGTCTCAGACATTGCAATTGCAGTAAGACAAGGTGCTGATGCTATCATGCTTTCAGGAGAAACTGCACATGGAAAgtgattttgctgttccttggtgacctttgttcttatattttatttttgttttagctgttcaaactttttttcaatattcatttt-ttactatttgtaatgcataag

upper sequence: GRMZM2G033526_T02 (Zea mays), 5'ss of exon 8
lower sequence: Vv02s0012g01170.t01 (Vitis vinifera), 5'ss of exon 8
ACCATCCTACTCCCACTAGGGCAGAAGTTTCTGACATAGCTATTGCAGTTCGGGAAGGTGCTGATGCCATCATGTTATCTGGCGAAACTGCTCATGGAAAgtaaggttcaacacttgttgctgtttaaatgtagtgttatcctaaacgctaaatggcaaaatagtcggtcacctgcagtttagccattatttgggttaaa----
| |||||||| || || ||||| ||||||||||| || || ||||| ||  | ||||||||||||||  | ||| | ||||| |||||||| |||||||||||||      | || | |    ||||   | |    || || ||     |  ||   |      | ||         |||    | | | |  ||||||    
ATCATCCTACACCAACAAGGGCCGAAGTTTCTGATATTGCAATTGCTGTAAGAGAAGGTGCTGATGCAGTTATGCTTTCTGGAGAAACTGCCCATGGAAAgtaagtc---gccctggctagcatttagtcgcatcaata-ccaaatttgaatttgtttatgctagcagtactaacttttttctttagtttcttagttaaaacag

upper sequence: GRMZM2G033526_T02 (Zea mays), 5'ss of exon 8
lower sequence: PP1S318_21V6.1 (Physcomitrella patens), 5'ss of exon 7
ACCATCCTACTCCCACTAGGGCAGAAGTTTCTGACATAGCTATTGCAGTTCGGGAAGGTGCTGATGCCATCATGTTATCTGGCGAAACTGCTCATGGAAAgtaag---gttcaacacttgttgctgtttaaatgtagtgttatcctaaacgctaaatggcaaaatagtcggtcacctgcagtttagccattatttgggttaaa-
  || ||||| |||||  | |||||||| || |||||||| || || || || |||||||| ||||| || ||| | || || ||||| ||||||||||||||||   | | ||  |      || | |      ||| || |  |   |   || |    ||||  | |     |     |      | | ||  ||   |  
CTCACCCTACGCCCACACGAGCAGAAGTCTCAGACATAGCCATCGCTGTCCGTGAAGGTGCGGATGCAATTATGCTTTCAGGGGAAACCGCTCATGGAAAgtaagcgcgattaaaccagtgcactatctctcgacagtttttttttctgcttgaagt----aaatttttgtgtttcgaatatcgtattactgttgaggacgatc

upper sequence: GRMZM2G033526_T02 (Zea mays), 5'ss of exon 8
lower sequence: PP1S205_25V6.1 (Physcomitrella patens), 5'ss of exon 7
ACCATCCTACTCCCACTAGGGCAGAAGTTTCTGACATAGCTATTGCAGTTCGGGAAGGTGCTGATGCCATCATGTTATCTGGCGAAACTGCTCATGGAAAgtaagg---ttcaacacttgttgctgtttaaatgtagtgttatcctaaacgctaaatggcaaaatagtcggtcacctgcagtttagccattatttgggttaaa
  || || ||||||||  | ||||| ||||| |||||||||||||| || || |||||||| || ||  | ||| | ||||| ||||| ||||| ||||||||||    ||    | |||||| |  |    | || | | ||| ||| | |  |       ||  | |       ||  |  |     ||||      |   
CTCACCCCACTCCCACACGAGCAGAGGTTTCAGACATAGCTATTGCCGTCCGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAAgtaagtacctttggaatttgttgatagtcttctttaatatcatc-taagctcatagcccagtaactgccaaaattttggggcatcaggcttatcgtcagtg--

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|22133857|gb|BQ833942.1|BQ833942
EST:     CGGGAAGGTGCTGATGCCATCATGTTATCTGGCGAAACTGCTCATGGAAA                         GTATCCACTAAAGGCAGTCAAGGTGATGCACACTGTGGCACTCAGAACAGA
genomic: CGGGAAGGTGCTGATGCCATCATGTTATCTGGCGAAACTGCTCATGGAAAgtaaggttca ... ctgtgtttagGTATCCACTAAAGGCAGTCAAGGTGATGCACACTGTGGCACTCAGAACAGA
EST: gi|26558430|gb|CA830665.1|CA830665
EST:     CGGGAAGGTGCTGATGCCATCATGTTATCTGGCGAAACTGCTCATGGAAA                         GTATCCACTAAAGGCAGTCAAGGTGATGCACACTGTGGCACTCAGAACAGA
genomic: CGGGAAGGTGCTGATGCCATCATGTTATCTGGCGAAACTGCTCATGGAAAgtaaggttca ... ctgtgtttagGTATCCACTAAAGGCAGTCAAGGTGATGCACACTGTGGCACTCAGAACAGA
EST: gi|32858382|gb|CD998063.1|CD998063
EST:     CGGGAAGGTGCTGATGCCATCATGTTATCTGGCGAAACTGCTCATGGAAA                         GTATCCACTAAAGGCAGTCAAGGTGATGCACACTGTGGCACTCAGAACAGA
genomic: CGGGAAGGTGCTGATGCCATCATGTTATCTGGCGAAACTGCTCATGGAAAgtaaggttca ... ctgtgtttagGTATCCACTAAAGGCAGTCAAGGTGATGCACACTGTGGCACTCAGAACAGA
EST: gi|22542067|gb|BU092505.1|BU092505
EST:     CGGGAAGGTGCTGATGCCATCATGTTATCTGGCGAAACTGCTCATGGAAA                         GTATCCACTAAAGGCAGTCAAGGTGATGCACACTGTGGCACTCAGAACAGA
genomic: CGGGAAGGTGCTGATGCCATCATGTTATCTGGCGAAACTGCTCATGGAAAgtaaggttca ... ctgtgtttagGTATCCACTAAAGGCAGTCAAGGTGATGCACACTGTGGCACTCAGAACAGA
EST: gi|31357830|gb|CD442187.1|CD442187
EST:     CGGGAAGGTGCTGATGCCATCATGTTATCTGGCGAAACTGCTCATGGAAA                         GTATCCACTAAAGGCAGTCAAGGTGATGCACACTGTGGCACTCAGAACAGA
genomic: CGGGAAGGTGCTGATGCCATCATGTTATCTGGCGAAACTGCTCATGGAAAgtaaggttca ... ctgtgtttagGTATCCACTAAAGGCAGTCAAGGTGATGCACACTGTGGCACTCAGAACAGA
EST: gi|87155458|gb|DY400247.1|DY400247
EST:     CGGGAAGGTGCTGATGCCATCATGTTATCTGGCGAAACTGCTCATGGAAA                         GTATCCACTAAAGGCAGTCAAGGTGATGCACACTGTGGCACTCAGAACAGA
genomic: CGGGAAGGTGCTGATGCCATCATGTTATCTGGCGAAACTGCTCATGGAAAgtaaggttca ... ctgtgtttagGTATCCACTAAAGGCAGTCAAGGTGATGCACACTGTGGCACTCAGAACAGA
EST: gi|60341691|gb|DN208664.1|DN208664
EST:     CGGGAAGGTGCTGATGCCATCATGTTATCTGGCGAAACTGCTCATGGAAA                         GTATCCACTAAAGGCAGTCAAGGTGATGCACACTGTGGCACTCAGAACAGA
genomic: CGGGAAGGTGCTGATGCCATCATGTTATCTGGCGAAACTGCTCATGGAAAgtaaggttca ... ctgtgtttagGTATCCACTAAAGGCAGTCAAGGTGATGCACACTGTGGCACTCAGAACAGA
EST: gi|60356976|gb|DN223949.1|DN223949
EST:     CGGGAAGGTGCTGATGCCATCATGTTATCTGGCGAAACTGCTCATGGAAA                         GTATCCACTAAAGGCAGTCAAGGTGATGCACACTGTGGCACTCAGAACAGA
genomic: CGGGAAGGTGCTGATGCCATCATGTTATCTGGCGAAACTGCTCATGGAAAgtaaggttca ... ctgtgtttagGTATCCACTAAAGGCAGTCAAGGTGATGCACACTGTGGCACTCAGAACAGA
EST: gi|67016939|gb|CO445688.1|CO445688
EST:     CGGGAAGGTGCTGATGCCATCATGTTATCTGGCGAAACTGCTCATGGAAA                         GTATCCACTAAAGGCAGTCAAGGTGATGCACACTGTGGCACTCAGAACAGA
genomic: CGGGAAGGTGCTGATGCCATCATGTTATCTGGCGAAACTGCTCATGGAAAgtaaggttca ... ctgtgtttagGTATCCACTAAAGGCAGTCAAGGTGATGCACACTGTGGCACTCAGAACAGA
EST: gi|76287860|gb|DV027428.1|DV027428
EST:     CCATCATGTTATCTGGCGAAACTGCTCATGGAAA                         GTATCCACTAAAGGCAGTCAAGGTGATGCACACTGTGGCACTCAGAACAGA
genomic: CCATCATGTTATCTGGCGAAACTGCTCATGGAAAgtaaggttca ... ctgtgtttagGTATCCACTAAAGGCAGTCAAGGTGATGCACACTGTGGCACTCAGAACAGA
EST: gi|67022089|gb|CO450838.1|CO450838
EST:     CGGGAAGGTGCTGATGCCATCATGTTATCTGGCGAAACTGCTCATGGAAA                         GTATCCACTAAAGGCAGTCAAGGTGATGCACACTGTGGCACTCAGAACAGA
genomic: CGGGAAGGTGCTGATGCCATCATGTTATCTGGCGAAACTGCTCATGGAAAgtaaggttca ... ctgtgtttagGTATCCACTAAAGGCAGTCAAGGTGATGCACACTGTGGCACTCAGAACAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACCATCCTACTCCCACTAGGGCAGAAGTTTCTGACATAGCTATTGCAGTTCGGGAAGGTGCTGATGCCATCATGTTATCTGGCGAAACTGCTCATGGAAAgtaaggttcaacacttgttgctgtttaaatgtagtgttatcctaaacgctaaatggcaaaatagtcggtcacctgcagtttagccattatttgggttaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA