Skip to another splice site:
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCACAGTCGGACAGTTTGTGTATGTGGTACGGAAGCGGATCAAGCTCAGCGCTGAGAAGGCAATCTTCATCTTCGTAAAGAACACCCTCCCACCAACAGgtaccggacagtagttccttctgttgtcataccagtgttggggaaaaataaaacaaaacctaccacggtgccccccgcccgtaacgttgttgtccctgcag

Basic information

species Zea mays
transcript GRMZM2G134613_T03
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G134613_T08 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os08g09240.1 (Oryza sativa), 5'ss of exon 5
CTCACAGTCGGACAGTTTGTGTATGTGGTACGGAAGCGGATCAAGCTCAGCGCTGAGAAGGCAATCTTCATCTTCGTAAAGAACACCCTCCCACCAACAGgtaccg-gacagtagttccttctgttgtcataccagtgttggggaaaaataaaacaaaacctaccacggtgccccccgcccgtaacgttgttgtccctgcag
||||| || ||||||||||||||||| || |||||||||||||||||||| |||||||||||||||||||||||||| |||||||| || |||||||||||||  |  | |  || ||     |   |||   ||   |      |||| ||||  | |  | |   | | ||       | |       |||  ||| |||
CTCACGGTTGGACAGTTTGTGTATGTTGTTCGGAAGCGGATCAAGCTCAGTGCTGAGAAGGCAATCTTCATCTTCGTCAAGAACACGCTTCCACCAACAGgtatggcaatatgagctctgggagcactcagttcaacatcaacataaaaaaaaatcataattgc-gtgatccctaaaatgccttgttgcattgctcctacag

upper sequence: GRMZM2G134613_T08 (Zea mays), 5'ss of exon 1
lower sequence: Vv19s0090g00580.t01 (Vitis vinifera), 5'ss of exon 5
CTCACAGTCGGACAGTTTGTGTATGTGGTACGGAAGCGGATCAAGCTCAGCGCTGAGAAGGCAATCTTCATCTTCGTAAAGAACACCCTCCCACCAACAGgtaccggacagtagttccttctgttgtc---ataccagtgttggggaaaaataaaacaaaacctaccacggt--gccccccgcccgtaacgttgt-tgtccctgcag
|| || || || |||||||| |||||| | |||||| |||||||||| || ||||||||||| || ||||| || || |||||    || ||||| || |||    || || | | | || |  | |    ||||   | | |  ||   |        |||     |   |       |      |    || | |||     |||
CTGACTGTTGGGCAGTTTGTTTATGTGATCCGGAAGAGGATCAAGCTTAGTGCTGAGAAGGCTATTTTCATTTTTGTCAAGAATGTTCTACCACCCACTGgtg--agaaagaattcctttttaatattcaaatacacatatcgatgatgtagtttctgtaactatttattatttatattcatttatttgtattttgtgttatcacag

upper sequence: GRMZM2G134613_T08 (Zea mays), 5'ss of exon 1
lower sequence: PP1S209_118V6.1 (Physcomitrella patens), 5'ss of exon 4
CTCACAGTCGGACAGTTTGTGTATGTGGTACGGAAGCGGATCAAGCTCAGCGCTGAGAAGGCAATCTTCATCTTCGTAAAGAACACCCTCCCACCAACAGgta--ccggacagtagttccttctgttgtcataccagtgttggggaaaa--ataaaacaaaacctac---cacggtgccccccgc--ccgtaacgttgttgtccctgcag----------------------------------------------------------------------------------------
 | || || |||||||||||||| ||| || ||||||| |||||| | ||  | |||||||| |||||||| ||||| ||||||   || || || |||||||    || | |  ||   | |    |  |   | ||| ||||  | |   |   |  | |  |     || ||        |     |    |  |||| |  |  ||                                                                                        
TTGACGGTTGGACAGTTTGTGTACGTGATAAGGAAGCGCATCAAGTTGAGTTCGGAGAAGGCCATCTTCATATTCGTGAAGAACGTGCTGCCCCCGACAGgtaggttgggcgggtgtgggtgcaagggagaaggc-gtggtgggttagattgtgggatgagagttggggacaaggaagtgggtgtagtggaggtgcggttggcggtagagagaggggtgcgtgggtttggttatgtcgggtgcgggattgttgtaagaaggttgtgtagtgaaaggagggagtggtgtgtggatgcag

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|116828492|gb|EC857917.1|EC857917
EST:     CGCTGAGAAGGCAATCTTCATCTTCGTAAAGAACACCCTCCCACCAACAG                         CTGCTCTGATGTCCGCCATCTACGAGGAGAACAAGGACGAGGACGGCTTCC
genomic: CGCTGAGAAGGCAATCTTCATCTTCGTAAAGAACACCCTCCCACCAACAGgtaccggaca ... gtccctgcagCTGCTCTGATGTCCGCCATCTACGAGGAGAACAAGGACGAGGACGGCTTCC
EST: gi|16921805|gb|BM075308.1|BM075308
EST:     CGCTGAGAAGGCAATCTTCATCTTCGTAAAGAACACCCTCCCACCAACAG                         CTGCTCTGATGTCCGCCATCTACGAGGAGAACAAGGACGAGGACGGCTTCC
genomic: CGCTGAGAAGGCAATCTTCATCTTCGTAAAGAACACCCTCCCACCAACAGgtaccggaca ... gtccctgcagCTGCTCTGATGTCCGCCATCTACGAGGAGAACAAGGACGAGGACGGCTTCC
EST: gi|71306764|gb|DR789543.1|DR789543
EST:     CGCTGAGAAGGCAATCTTCATCTTCGTAAAGAACACCCTCCCACCAACAG                         CTGCTCTGATGTCCGCCATTTACGAGGAGAACAAGGACGAGGACGGCTTCC
genomic: CGCTGAGAAGGCAATCTTCATCTTCGTAAAGAACACCCTCCCACCAACAGgtaccggaca ... gtccctgcagCTGCTCTGATGTCCGCCATCTACGAGGAGAACAAGGACGAGGACGGCTTCC
EST: gi|71306765|gb|DR789544.1|DR789544
EST:     CGCTGAGAAGGCAATCTTCATCTTCGTAAAGAACACCCTCCCACCAACAG                         CTGCTCTGATGTCCGCCATCTACGAGGAGAACAAGGACGAGGACGGCTTCC
genomic: CGCTGAGAAGGCAATCTTCATCTTCGTAAAGAACACCCTCCCACCAACAGgtaccggaca ... gtccctgcagCTGCTCTGATGTCCGCCATCTACGAGGAGAACAAGGACGAGGACGGCTTCC
EST: gi|37386976|gb|CF630680.1|CF630680
EST:     CGCTGAGAAGGCAATCTTCATCTTCGTAAAGAACACCCTCCCACCAACAG                         CTGCTCTGATGTCCGCCATCTACGAGGAGAACAAGGACGAGGACGGCTTCC
genomic: CGCTGAGAAGGCAATCTTCATCTTCGTAAAGAACACCCTCCCACCAACAGgtaccggaca ... gtccctgcagCTGCTCTGATGTCCGCCATCTACGAGGAGAACAAGGACGAGGACGGCTTCC
EST: gi|16925527|gb|BM078595.1|BM078595
EST:     CGCTGAGAAGGCAATCTTCATCTTCGTAAAGAACACCCTCCCACCAACAG                         CTGCTCTGATGTCCGCCATCTACGAGGAGAACAAGGACGAGGACGGCTTCC
genomic: CGCTGAGAAGGCAATCTTCATCTTCGTAAAGAACACCCTCCCACCAACAGgtaccggaca ... gtccctgcagCTGCTCTGATGTCCGCCATCTACGAGGAGAACAAGGACGAGGACGGCTTCC
EST: gi|67025573|gb|CO454322.1|CO454322
EST:     CGCTGAGAAGGCAATCTTCATCTTCGTAAAGAACACCCTCCCACCAACAG                         CTGCTCTGATGTCCGCCATCTACGAGGAGAACAAGGACGAGGACGGCTTCC
genomic: CGCTGAGAAGGCAATCTTCATCTTCGTAAAGAACACCCTCCCACCAACAGgtaccggaca ... gtccctgcagCTGCTCTGATGTCCGCCATCTACGAGGAGAACAAGGACGAGGACGGCTTCC
EST: gi|84980814|gb|DW531163.1|DW531163
EST:     CGCTGAGAAGGCAATCTTCATCTTCGTAAAGAACACCCTCCCACCAACAG                         CTGCTCTGATGTCTGCCATCTACGAGGAGAACAAGGACGAGGACGGCTTCC
genomic: CGCTGAGAAGGCAATCTTCATCTTCGTAAAGAACACCCTCCCACCAACAGgtaccggaca ... gtccctgcagCTGCTCTGATGTCCGCCATCTACGAGGAGAACAAGGACGAGGACGGCTTCC
EST: gi|211145629|gb|FL256802.1|FL256802
EST:     CGCTGAGAAGGCAATCTTCATCTTCGTAAAGAACACCCTCCCACCAACAG                         CTGCTCTGATGTCTGCCATCTACGAGGAGAACAAGGACGAGGACGGCTTCC
genomic: CGCTGAGAAGGCAATCTTCATCTTCGTAAAGAACACCCTCCCACCAACAGgtaccggaca ... gtccctgcagCTGCTCTGATGTCCGCCATCTACGAGGAGAACAAGGACGAGGACGGCTTCC
EST: gi|18168853|gb|BM338693.1|BM338693
EST:     CGCTGAGAAGGCAATCTTCATCTTCGTAAAGAACACCCTCCCACCAACAG                         CTGCTCTAATGTCCGCCATCTACGAGGAGAACAAGGACGAGGACGGCTTCC
genomic: CGCTGAGAAGGCAATCTTCATCTTCGTAAAGAACACCCTCCCACCAACAGgtaccggaca ... gtccctgcagCTGCTCTGATGTCCGCCATCTACGAGGAGAACAAGGACGAGGACGGCTTCC
EST: gi|37374696|gb|CF623730.1|CF623730
EST:     CGCTGAGAAGGCAATCTTCATCTTCGTAAAGAACACCCTCCCACCAACAG                         CTGCTCTGATGTCCGCCATCTACGAGGAGAACAAGGACGAGGACGGCTTCC
genomic: CGCTGAGAAGGCAATCTTCATCTTCGTAAAGAACACCCTCCCACCAACAGgtaccggaca ... gtccctgcagCTGCTCTGATGTCCGCCATCTACGAGGAGAACAAGGACGAGGACGGCTTCC
EST: gi|67040113|gb|CO466368.1|CO466368
EST:     CGCTGAGAAGGCAATCTTCATCTTCGTAAAGAACACCCTCCCACCAACAG                         CTGCTCTGATGTCCGCCATCTACGAGGAGAACAAGGACGAGGACGGCTTCC
genomic: CGCTGAGAAGGCAATCTTCATCTTCGTAAAGAACACCCTCCCACCAACAGgtaccggaca ... gtccctgcagCTGCTCTGATGTCCGCCATCTACGAGGAGAACAAGGACGAGGACGGCTTCC
EST: gi|37391661|gb|CF633074.1|CF633074
EST:     CGCTGAGAAGGCAATCTTCATCTTCGTAAAGAACACCCTCCCACCAACAG                         CTGCTCTGATGTCCGCCATCTACGAGGAGAACAAGGACGAGGACGGCTTCC
genomic: CGCTGAGAAGGCAATCTTCATCTTCGTAAAGAACACCCTCCCACCAACAGgtaccggaca ... gtccctgcagCTGCTCTGATGTCCGCCATCTACGAGGAGAACAAGGACGAGGACGGCTTCC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 81

CTCACAGTCGGACAGTTTGTGTATGTGGTACGGAAGCGGATCAAGCTCAGCGCTGAGAAGGCAATCTTCATCTTCGTAAAGAACACCCTCCCACCAACAGgtaccggaca ... gtccctgcagCTGCTCTGATGTCCGCCATCTACGAGGAGAACAAGGACGAGGACGGCTTCCTCTACATGACGTACAGCGGCGAGAACACCTTCGGGCTGTTCTGAGTGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 629

CTCACAGTCGGACAGTTTGTGTATGTGGTACGGAAGCGGATCAAGCTCAGCGCTGAGAAGGCAATCTTCATCTTCGTAAAGAACACCCTCCCACCAACAGgtaccggaca ... gtccctgcagCTGCTCTGATGTCCGCCATCTACGAGGAGAACAAGGACGAGGACGGCTTCCTCTACATGACGTACAGCGGCGAGAACACCTTCGGGCTGTTCTGAGTGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 622

CTCACAGTCGGACAGTTTGTGTATGTGGTACGGAAGCGGATCAAGCTCAGCGCTGAGAAGGCAATCTTCATCTTCGTAAAGAACACCCTCCCACCAACAGgtaccggaca ... gtccctgcagCTGCTCTGATGTCCGCCATCTACGAGGAGAACAAGGACGAGGACGGCTTCCTCTACATGACGTACAGCGGCGAGAACACCTTCGGGCTGTTCTGAGTGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 330

CTCACAGTCGGACAGTTTGTGTATGTGGTACGGAAGCGGATCAAGCTCAGCGCTGAGAAGGCAATCTTCATCTTCGTAAAGAACACCCTCCCACCAACAGgtaccggaca ... gtccctgcagCTGCTCTGATGTCCGCCATCTACGAGGAGAACAAGGACGAGGACGGCTTCCTCTACATGACGTACAGCGGCGAGAACACCTTCGGGCTGTTCTGAGTGGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCACAGTCGGACAGTTTGTGTATGTGGTACGGAAGCGGATCAAGCTCAGCGCTGAGAAGGCAATCTTCATCTTCGTAAAGAACACCCTCCCACCAACAGgtaccggacagtagttccttctgttgtcataccagtgttggggaaaaataaaacaaaacctaccacggtgccccccgcccgtaacgttgttgtccctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC