RetrogeneDB ID: retro_itri_428

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393291.1:418751..419933(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000024007
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MDM4
• Ensembl ID: ENSSTOG00000004184
• Aliases: None
• Description: Mdm4 p53 binding protein homolog (mouse) [Source:HGNC Symbol;Acc:6974]

Sequence

>retro_itri_428
AGCCCTCTCTATGATATGCTAAGAAAGAATCTTGTCACTTTAACCACTGATACTACAGATGCTGCTCAGACTCTCGCTCT
CGCACAGGATCACAGTTTGGATATTCCAAGTCAAGACCAACCCAAGCAAAGTGCAGAGGAAAGTTCTAATTCCAGGAAAA
GAATTGAAGAGGGTGATATTCCTGCACTGCCCACCTCAGAGCATAAATGCAAAAATTCTAGAGAAGATGAAGACTTGATA
AATTTAAGCCAAGATGAGACATCTAGGTTGGACCTTGAGTTTGAGGAGTGGGATGTAGCTGGCCTGCCTTGGTTGTTTTT
AGGAAACTTGAGAAACAACTATACACCCAGAAGTAATGGCTCAACTGATTTACAGACAAATCAGGATATAGGTACTGCCA
TTGTTTCAGATACTACAGATGATTTGTGGTTTTTAAATGAGTCAGTTTCAGAGCAGTTAGGTGTTGGAATAAAAGTTGAA
GCTGCTGATACTGAACAAGCAAGTGAAGAAGTAGGGAAAGTGAGTGACAAAAAGGTGATTGAAGTGGGGAAAAATGATGA
CCGTGAGGACTCTAAGTCCTTAAGTGATGATACTGATATAGAAGTTACCTCTGAGGATGAGTGGCAGTGTACTGAATGCA
AGAAATTTAATTCTCCAAGCAAAAGGTACTGTTTCCATTGCTGGGCCTTGAGGAAGGACTGGTATTCAGATTGTTCTAAA
TTAACACATTCTCTCTCCACATCTGACATCACTGCCGTGCCCGAAAAGAAGGAAAGTGAAGGAATTGATGTCCCTAATTG
CCGAAGAACTGTTTCAGCTCCAGTTGTTAGACCTAAAGATGTATCTATAAAGGAAGGAAATTCTAAACTTTTAAATCCCT
GCAACTCAGTGGAATTCTTGGATTTGGCTCACAGTTCTGAAAGCCAGACCATCTTAAGTATGGGAGAACAATCAGATAAC
GTCTCTGAGCAGAGAACAGATGTAGAAAATATGGAGGATTGCCAGAATATCTTGAAGCCATGTAGCTTGTGTGAGAAAAG
ACCACAAGATGGGAATATTATTCATGGAAGGACAAGCCATCTTACGACTTGTTTTCCCTGTGCCAGAAGACTAAAGAAGG
CTGGGGCTTCATGTCCTATTTGCAAGAAAGAGATTCAATTAGTTATTAAGGTTTTTAAAGCA

Alignment

ORF - retro_itri_428 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.95 %
• Parental protein coverage: 80.61 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SPLYDMLRKNLVTLSTATTDAAQTLALAQDHSLDIPSQDQPKQSTEESSNSRKRIEEGDIPALPTSEHKC
          SPLYDMLRKNLVTL.T.TTDAAQTLALAQDHSLDIPSQDQPKQS.EESSNSRKRIEEGDIPALPTSEHKC
Retrocopy SPLYDMLRKNLVTLTTDTTDAAQTLALAQDHSLDIPSQDQPKQSAEESSNSRKRIEEGDIPALPTSEHKC

Parental  RNSREDEDLINLSQDDTSRLDLGFEEWDVAGLPWWFLGNLRNNYTPRSNGSTDLQTNQDIGTAIVSDTTD
          .NSREDEDLINLSQD.TSRLDL.FEEWDVAGLPW.FLGNLRNNYTPRSNGSTDLQTNQDIGTAIVSDTTD
Retrocopy KNSREDEDLINLSQDETSRLDLEFEEWDVAGLPWLFLGNLRNNYTPRSNGSTDLQTNQDIGTAIVSDTTD

Parental  DLWFLNESVSEQLGVGIKVEAADTEQASEEVGKVSDKKVIEVGKNDDLEDSKSLSDDTDIEVTSEDEWQC
          DLWFLNESVSEQLGVGIKVEAADTEQASEEVGKVSDKKVIEVGKNDD.EDSKSLSDDTDIEVTSEDEWQC
Retrocopy DLWFLNESVSEQLGVGIKVEAADTEQASEEVGKVSDKKVIEVGKNDDREDSKSLSDDTDIEVTSEDEWQC

Parental  TECKKFNSPSKRYCFRCWALRKDWYSDCSKLTHSLSTSDITAVPEKKESEGIDVPDCRRTVSAPVVRPKD
          TECKKFNSPSKRYCF.CWALRKDWYSDCSKLTHSLSTSDITAVPEKKESEGIDVP.CRRTVSAPVVRPKD
Retrocopy TECKKFNSPSKRYCFHCWALRKDWYSDCSKLTHSLSTSDITAVPEKKESEGIDVPNCRRTVSAPVVRPKD

Parental  VSIKEGNSKLLNPCNSVEFLDLAHSSESQETISSMGEQSDNISEQRTDVENVEDCQNILKPCSLCEKRPR
          VSIKEGNSKLLNPCNSVEFLDLAHSSESQ.TI.SMGEQSDN.SEQRTDVEN.EDCQNILKPCSLCEKRP.
Retrocopy VSIKEGNSKLLNPCNSVEFLDLAHSSESQ-TILSMGEQSDNVSEQRTDVENMEDCQNILKPCSLCEKRPQ

Parental  DGNIIHGRTSHLTTCFPCARRLKKAGASCPICKKEIQLVIKVFIA
          DGNIIHGRTSHLTTCFPCARRLKKAGASCPICKKEIQLVIKVF.A
Retrocopy DGNIIHGRTSHLTTCFPCARRLKKAGASCPICKKEIQLVIKVFKA

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_428 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_428 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001126	1 retrocopy	retro_amel_1730,
Mus musculus	ENSMUSG00000054387	1 retrocopy	retro_mmus_3520,
Otolemur garnettii	ENSOGAG00000011679	1 retrocopy	retro_ogar_1852,
Ictidomys tridecemlineatus	ENSSTOG00000004184	1 retrocopy	retro_itri_428 ,
Ictidomys tridecemlineatus	ENSSTOG00000014702	1 retrocopy	retro_itri_1731,