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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACATCGCGGAGCAGTTCGGCAGCTGCTGGGCGTCGTTCCGGCCGCAGTACATGATCGGCTCCGGCAACAACAAGGACTGCGAGGAGTGGTTCTTCGACAgtaataaacagcccagccttggattcattctcattattctcctctcttctccgacgaccatgacgacctccatggtccgtccatgcag

Basic information

species Zea mays
transcript GRMZM2G111216_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G111216_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os07g11110.1 (Oryza sativa), 5'ss of exon 4
---TACATCGCGGAGCAGTTCGGCAGCTGCTGGGCGTCGTTCCGGCCGCAGTACATGATCGGCTCCGGCAACAACAAGGACTGCGAGGAGTGGTTCTTCGACAgtaataaacagcccag---ccttggattcattctcattattctcctctcttctccgacgaccatgacgacctccatggtccgtccatgcag----------
   ||||||||||||||||||||||||||   ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| || || || |    ||        ||||||   | | ||    |  | |  || ||  |    |  |  | |         |  |           
AAGTACATCGCGGAGCAGTTCGGCAGCTG---GGCGTCGTTCCGGCCGCAGTACATGATCGGCTCCGGCAACAACAAGGACTGCGAGGAGTGGTTCTTCGACAgtaa-aatcacccaaatccccccaaccaaattctcccaaatttcaaaccgccccaaacaacattcttcaatttgaagacaaaattgtcaatttttttactg

upper sequence: GRMZM2G111216_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA10G03200.1 (Glycine max), 5'ss of exon 4
---TACATCGCGGAGCAGTTCGGCAGCTGCTGGGCGTCGTTCCGGCCGCAGTACATGATCGGCTCCGGCAACAACAAGGACTGCGAGGAGTGGTTCTTCGACAgtaa------------taaacagcc--cagccttggattcattctcattattctcctctcttctccgacgaccatgacgacctccatggtccgtc-catgcag
   ||||| |  ||    |  || || ||   |||   ||||||||| ||||||||||| || || ||||||||||| ||||| ||||||||||| || ||||||||            ||||||  |   |   ||   || |    |||      |||   |||    | |   |   | | |  ||   ||  |  ||||   
AAATACATTGAAGAAACTTATGGAAGTTG---GGCAGTGTTCCGGCCACAGTACATGATTGGGTCTGGCAACAACAAAGACTGTGAGGAGTGGTTTTTTGACAgtaaggggaactttcttaaacaaacgttattattaactttaaatacatatgaagccttgtttcaataaagtgaagtgctaacaacacactctctaacatg---

upper sequence: GRMZM2G111216_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA02G16620.1 (Glycine max), 5'ss of exon 4
---TACATCGCGGAGCAGTTCGGCAGCTGCTGGGCGTCGTTCCGGCCGCAGTACATGATCGGCTCCGGCAACAACAAGGACTGCGAGGAGTGGTTCTTCGACAgtaataaa-------cagcccagccttgg-attcattctcattattctcc-----tctcttctccgacgaccatgacgacctccatggtccgtccatgcag-------------------------
   ||||| |  ||    || || || ||   |||   ||||||||| ||||||||||| || || |||||||| || ||||| ||||||||||| || ||||||||            |  | | | ||   |||   | | | || |         ||  |  | | |  |  |       ||  | ||  |     |  |                          
AAATACATTGAAGAAACCTTTGGAAGTTG---GGCAGTGTTCCGGCCACAGTACATGATTGGGTCTGGCAACAATAAAGACTGTGAGGAGTGGTTTTTTGACAgtaaggggaactttctaaacaaactttattattagcttttaatactacatatgaatccttgtttcaataaataatcttttctagaaggatcaatactaaaaacaatgtgcaatgtcatatttgtag

upper sequence: GRMZM2G111216_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT3G63140.1 (Arabidopsis thaliana), 5'ss of exon 4
---TACATCGCGGAGCAGTTCGGCAGCTGCTGGGCGTCGTTCCGGCCGCAGTACATGATCGGCTCCGGCAACAACAAGGACTGCGAGGAGTGGTTCTTCGACAgtaa-taaacagcccagccttggattcattctcattattctcctctcttctccgacgaccatgacgacctccatggtccgtccatgcag
   ||| | || ||    ||||| | |||   ||| || || || |||||||||||||||||||| ||||||||||| |||||||| || |||||||||||| |||| |      | || ||   ||||      ||          | | |     | |      | |   |||  |              
AAGTACTTAGCCGAAACATTCGGGAACTG---GGCCTCCTTTCGACCGCAGTACATGATCGGCTCTGGCAACAACAAAGACTGCGAAGAATGGTTCTTCGACCgtaagtctctcacacacccaaagatttcaatacaaagacaaaaacacgt----aatggttgaaatgtgttcccag--------------

upper sequence: GRMZM2G111216_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv07s0104g00510.t01 (Vitis vinifera), 5'ss of exon 4
---TACATCGCGGAGCAGTTCGGCAGCTGCTGGGCGTCGTTCCGGCCGCAGTACATGATCGGCTCCGGCAACAACAAGGACTGCGAGGAGTGGTTCTTCGACAgtaa-taaacagcccagc-------cttggattcattctcattattctcctctcttctccgacgaccatgacgacctcca---tggtccg-tccatgcag
   |||||  | |||   |||||||||||   |||    ||||| |||||||||||||| || || || |||||||| || || |||||||||||||| ||| ||||   || | ||  ||        ||| | |  || | |     || |  || ||| | |   ||    | |  | ||   || |||| ||    |||
ACATACATTTCAGAGGTTTTCGGCAGCTG---GGCAATTTTCCGTCCGCAGTACATGATTGGATCTGGAAACAACAAAGATTGTGAGGAGTGGTTCTTTGACCgtaagcgaataaccttgcgcattggtttgaactttttgtaacacagctgcattcatcttcaaaatcccctgccattttcacattgatccgctctgaacag

upper sequence: GRMZM2G111216_T01 (Zea mays), 5'ss of exon 4
lower sequence: PP1S55_140V6.1 (Physcomitrella patens), 5'ss of exon 4
TACATCGCGGAGCAGTTCGGCAGCTGCTGGGCGTCGTTCCGGCCGCAGTACATGATCGGCTCCGGCAACAACAAGGACTGCGAGGAGTGGTTCTTCGACAgtaataaacagcccagccttgga--ttcattctcattattctcctctcttctccgacgaccatgacgacc----tccatggtccgtccatgcag----------------
||  | |||||   |  |      | |||||| || ||||| || |||||||||| |||   ||| ||||||||||| ||||| || ||||||||||||||| |  |       | |||| |   |||||  |||  |   ||      |      | ||   ||  |      ||  ||||  |  ||||  |                
TATCTGGCGGAATTGGGCTTAGAGTCCTGGGCCTCATTCCGACCTCAGTACATGACCGGAGACGGGAACAACAAGGATTGCGAAGAATGGTTCTTCGACAgtgagtatt--ttaaaccttcgtctttcatgttcaccaagttcaatctctggaaagctacttcgataagtgtggtcagtggta-gctcatgttgagtcgaaattttacag

upper sequence: GRMZM2G111216_T01 (Zea mays), 5'ss of exon 4
lower sequence: EFJ07659 (Selaginella moellendorffii), 5'ss of exon 4
TACATCGCGGAGCAGTTCGGCAGCTGCTGGGCGTCGTTCCGGCCGCAGTACATGATCGGCTCCGGCAACAACAAGGACTGCGAGGAGTGGTTCTTCGACAgtaataaacagcccagccttggattcattctcattattctcctctcttctccgacgaccatgacgacctccatggtccgtccatgcag
|||||  |  |   |     ||  |  ||  | |||||  | || ||||||||||  |||||||| |||||||||||||||||||| ||||| |||||||||||                       || || |  |||   ||   | ||    || |||||  || ||  ||| | |         
TACATTTCAAAATTGGCTTTCAAGTTTTGCTCCTCGTTTAGACCCCAGTACATGACTGGCTCCGGGAACAACAAGGACTGCGAGGAATGGTTTTTCGACAgtaagt---------------------ttttcctccttccgttcgtgtttcaagggatcatgaaaacttct-tggacag---------

upper sequence: GRMZM2G111216_T01 (Zea mays), 5'ss of exon 4
lower sequence: EFJ07715 (Selaginella moellendorffii), 5'ss of exon 4
TACATCGCGGAGCAGTTCGGCAGCTGCTGGGCGTCGTTCCGGCCGCAGTACATGATCGGCTCCGGCAACAACAAGGACTGCGAGGAGTGGTTCTTCGACAgtaataaacagcccagccttggattcattctcattattctcctctcttctccgacgaccatgacgacctccatggtccgtccatgcag
|||||  |  ||  |     ||  |  ||| | |||||  | || ||||||||||  |||||||| |||||||||||||||||||| ||||| |||||||||||           ||          || || || ||||  ||   | ||    || |||||  || |   ||| | |         
TACATTTCAAAGTCGGCTTTCAAGTTTTGGTCCTCGTTTAGACCCCAGTACATGACTGGCTCCGGGAACAACAAGGACTGCGAGGAATGGTTTTTCGACAgtaa-----------gc----------ttttccttcttctgttcgtgtttcaagggatcatgaaaacgttt-tggacag---------

upper sequence: GRMZM2G111216_T01 (Zea mays), 5'ss of exon 4
lower sequence: EFJ07654 (Selaginella moellendorffii), 5'ss of exon 4
TACATCGCGGAGCAGTTCGGCAGCTGCTGGGCGTCGTTCCGGCCGCAGTACATGATCGGCTCCGGCAACAACAAGGACTGCGAGGAGTGGTTCTTCGACAgtaataaacagcccagccttggattcattctcattattctcctctcttctccgacgaccatgacgacctccatggtccgtccatgcag
|||||  |  ||  |     ||  |  ||| | |||||  | || ||||||||||  |||||||| |||||||||||||||||||| ||||| |||||||||||                       || || |  |||   ||   | ||    || |||||  || |   ||| | |         
TACATTTCAAAGTCGGCTTTCAAGTTTTGGTCCTCGTTTAGACCACAGTACATGACTGGCTCCGGGAACAACAAGGACTGCGAGGAATGGTTTTTCGACAgtaagt---------------------ttttcctccttcctttcgtgtttcaagggatcatgaaaacgttt-tggacag---------

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|149105826|gb|EE291422.2|EE291422
EST:     CATGATCGGCTCCGGCAACAACAAGGACTGCGAGGAGTGGTTCTTCGACA                         GGATCGTGCGGAACCGGCCGGTGCCGATCCCGGGGAACGGGATGCAGCTGA
genomic: CATGATCGGCTCCGGCAACAACAAGGACTGCGAGGAGTGGTTCTTCGACAgtaataaaca ... gtccatgcagGGATCGTGCGGAACCGGCCGGTGCCGATCCCGGGGAACGGGATGCAGCTGA
EST: gi|149082554|gb|EE171749.2|EE171749
EST:     CATGATCGGCTCCGGCAACAACAAGGACTGCGAGGAGTGGTTCTTCGACA                         GGATCGTGCGGAACCGGCCGGTGCCGATCCCGGGGAACGGGATGCAGCTGA
genomic: CATGATCGGCTCCGGCAACAACAAGGACTGCGAGGAGTGGTTCTTCGACAgtaataaaca ... gtccatgcagGGATCGTGCGGAACCGGCCGGTGCCGATCCCGGGGAACGGGATGCAGCTGA
EST: gi|71763125|gb|DR961062.1|DR961062
EST:     CATGATCGGCTCCGGCAACAACAAGGACTGCGAGGAGTGGTTCTTCGACA                         GGATCGTGCGGAACCGGCCGGTGCCGATCCCGGGGAACGGGATGCAGCTGA
genomic: CATGATCGGCTCCGGCAACAACAAGGACTGCGAGGAGTGGTTCTTCGACAgtaataaaca ... gtccatgcagGGATCGTGCGGAACCGGCCGGTGCCGATCCCGGGGAACGGGATGCAGCTGA
EST: gi|149094578|gb|EE180104.2|EE180104
EST:     CATGATCGGCTCCGGCAACAACAAGGACTGCGAGGAGTGGTTCTTCGACA                         GGATCGTGCGGAACCGGCCGGTGCCGATCCCGGGGAACGGGATGCAGCTGA
genomic: CATGATCGGCTCCGGCAACAACAAGGACTGCGAGGAGTGGTTCTTCGACAgtaataaaca ... gtccatgcagGGATCGTGCGGAACCGGCCGGTGCCGATCCCGGGGAACGGGATGCAGCTGA
EST: gi|71448832|gb|DR829882.1|DR829882
EST:     CATGATCGGCTCCGGCAACAACAAGGACTGCGAGGAGTGGTTCTTCGACA                         GGATCGTGCGGAACCGGCCGGTGCCGATCCCGGGGAACGGGATGCAGCTGA
genomic: CATGATCGGCTCCGGCAACAACAAGGACTGCGAGGAGTGGTTCTTCGACAgtaataaaca ... gtccatgcagGGATCGTGCGGAACCGGCCGGTGCCGATCCCGGGGAACGGGATGCAGCTGA
EST: gi|37416734|gb|CF646020.1|CF646020
EST:     CATGATCGGCTCCGGCAACAACAAGGACTGCGAGGAGTGGTTCTTCGACA                         GGATCGTGCGGAACCGGCCGGTGCCGATCCCGGGGAACGGGATGCAGCTGA
genomic: CATGATCGGCTCCGGCAACAACAAGGACTGCGAGGAGTGGTTCTTCGACAgtaataaaca ... gtccatgcagGGATCGTGCGGAACCGGCCGGTGCCGATCCCGGGGAACGGGATGCAGCTGA

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 1 RNA-Seqlibrary.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 14

TACATCGCGGAGCAGTTCGGCAGCTGCTGGGCGTCGTTCCGGCCGCAGTACATGATCGGCTCCGGCAACAACAAGGACTGCGAGGAGTGGTTCTTCGACAgtaataaaca ... gtccatgcagGGATCGTGCGGAACCGGCCGGTGCCGATCCCGGGGAACGGGATGCAGCTGACCAACGTGGCGCACGTCCGGGACCTGTCCAGCATGCTGTCGCTGGCCGT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACATCGCGGAGCAGTTCGGCAGCTGCTGGGCGTCGTTCCGGCCGCAGTACATGATCGGCTCCGGCAACAACAAGGACTGCGAGGAGTGGTTCTTCGACAgtaataaacagcccagccttggattcattctcattattctcctctcttctccgacgaccatgacgacctccatggtccgtccatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG