RetrogeneDB ID: retro_mmus_2247

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:47050384..47051641(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000072387
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ikzf5
• Ensembl ID: ENSMUSG00000040167
• Aliases: Ikzf5, 2610034F18Rik, PEGASUS, Zfpn1a5
• Description: IKAROS family zinc finger 5 [Source:MGI Symbol;Acc:MGI:1914393]

Sequence

>retro_mmus_2247
ATGGGTGAAAAGAAACCAGAGCCTTTGGACTTTGTAAAAGATTTCCCGGAATACCTGACCCAGCAGACGCATCATGTGAA
CATGATTTCGGGATCTGTTAGTGGGGACAAAGAAGCAGAGACTCTTCAGGGAGCTGAAGCAGATGGCGATCAAAATGGCC
TTGATCACCCGTCTGTTGAAGTTTCCCTGGATGAAAACTCAGGAATGTTAGTAGACGGGTTTGAGAGGACCTTCGATGGG
AAGCTCAAGTGTCGGTACTGCAACTATGCCAGCAAAGGAACGGCCAGGCTCATTGAGCACATCAGGATCCACACAGGCGA
GAAGCCTCACAGGTGTCACTTATGTCCATTTGCATCTGCTTACGAGCGCCACCTGGAATCCCATATGCGCTCTCACACTG
GGGAAAAACCATACAAATGTGAATTGTGCTCCTTCTGCTGCAGTGACCGAAGTAACCTGTCCCACCATCGAAGGCGCAAA
CATAAAATGGTACCAATTAAAGGTACCAGGTCTTCCTTAAGCAGCAAGAAAATGTGGGGGGTTTTACAAAAGAAAACAAG
CAATCTGGGGTATAGCAGAAGAGCACTAATCAACTTAAGTCCACCTTCCATGGTGGTCCAGAAACCAGACTACCTTAATG
ATTTTACACACGAAATCCCAAATATTCAGACTGACTCCTATGAAGCTATGGCTAAAACTACACCAACTGGTGGCCTGCCA
AGGGACCCCCAAGAACTCATGGTTGACAACCCTTTGAATCAGCTCTCTACTTTAGCAGGACAGTTCTCCAGCTTGCCACC
AGAAAACCAAAACCCTGCCTCTCCTGATGTAGATGCCTGCCCTGATGAAAAGCCTTTCATGATTCAGCAACCCTCTGCCC
AAGCAGTTGTCTCTGCTGTGTCAGCAAGTATTCCTCAGAGCTCCTCCCCCACAAGTCCGGAACCGTGGCCATCACATAGT
CAGAGGAACTACAGTCCAGTGGCAGGGCCCAGCAGTGAACCAAGTGCCCACACCAGTACTCCCAGCATAGGAAACAGCCA
GCCAAGCACTCCAGCTCCAACCCTGCCGGTGCAGGATCCTCAGCTTCTACACCACTGCCAGCACTGTGACGTGTACTTTG
CAGACAACGTCCTTTACACTGTCCATATGGGGTGCCATGGGTATGACAGCCCCTTTCAGTGTAACGTATGTGGGTACAAA
TGTAAAGACAAGTACGATTTTGCCTGTCATTTTGCAAGAGGGCAACACAACCAGCAC

Alignment

ORF - retro_mmus_2247 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.09 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGEKKPEPLDFVKDFQEYLTQQTHHVNMISGSVSGDKEAETLQGAGTDGDQNGLDHPSVEVSLDENSGML
          MGEKKPEPLDFVKDF.EYLTQQTHHVNMISGSVSGDKEAETLQGA..DGDQNGLDHPSVEVSLDENSGML
Retrocopy MGEKKPEPLDFVKDFPEYLTQQTHHVNMISGSVSGDKEAETLQGAEADGDQNGLDHPSVEVSLDENSGML

Parental  VDGFERTFDGKLKCRYCNYASKGTARLIEHIRIHTGEKPHRCHLCPFASAYERHLEAHMRSHTGEKPYKC
          VDGFERTFDGKLKCRYCNYASKGTARLIEHIRIHTGEKPHRCHLCPFASAYERHLE.HMRSHTGEKPYKC
Retrocopy VDGFERTFDGKLKCRYCNYASKGTARLIEHIRIHTGEKPHRCHLCPFASAYERHLESHMRSHTGEKPYKC

Parental  ELCSFRCSDRSNLSHHRRRKHKMVPIKGTRSSLSSKKMWGVLQKKTSNLGYSRRALINLSPPSMVVQKPD
          ELCSF.CSDRSNLSHHRRRKHKMVPIKGTRSSLSSKKMWGVLQKKTSNLGYSRRALINLSPPSMVVQKPD
Retrocopy ELCSFCCSDRSNLSHHRRRKHKMVPIKGTRSSLSSKKMWGVLQKKTSNLGYSRRALINLSPPSMVVQKPD

Parental  YLNDFTHEIPNIQTDSYEAMAKTTPTGGLPRDPQELMVDNPLNQLSTLAGQLSSLPPENQNPASPDVDAC
          YLNDFTHEIPNIQTDSYEAMAKTTPTGGLPRDPQELMVDNPLNQLSTLAGQ.SSLPPENQNPASPDVDAC
Retrocopy YLNDFTHEIPNIQTDSYEAMAKTTPTGGLPRDPQELMVDNPLNQLSTLAGQFSSLPPENQNPASPDVDAC

Parental  PDEKPFMIQQPSAQAVVSAVSASIPQSSSPTSPEPRPSHSQRNYSPVAGPSSEPSAHTSTPSIGNSQPST
          PDEKPFMIQQPSAQAVVSAVSASIPQSSSPTSPEP.PSHSQRNYSPVAGPSSEPSAHTSTPSIGNSQPST
Retrocopy PDEKPFMIQQPSAQAVVSAVSASIPQSSSPTSPEPWPSHSQRNYSPVAGPSSEPSAHTSTPSIGNSQPST

Parental  PAPTLPVQDPQLLHHCQHCDVYFADNVLYTVHMGCHGYDSPFQCNVCGCKCKDKYDFACHFARGQHNQH
          PAPTLPVQDPQLLHHCQHCDVYFADNVLYTVHMGCHGYDSPFQCNVCG.KCKDKYDFACHFARGQHNQH
Retrocopy PAPTLPVQDPQLLHHCQHCDVYFADNVLYTVHMGCHGYDSPFQCNVCGYKCKDKYDFACHFARGQHNQH

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.07 RPM	16.45 RPM
SRP007412_cerebellum	0.26 RPM	16.33 RPM
SRP007412_heart	0.06 RPM	13.17 RPM
SRP007412_kidney	0.15 RPM	11.70 RPM
SRP007412_liver	0.11 RPM	5.71 RPM
SRP007412_testis	0.32 RPM	7.41 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2247 was not detected

EST

No EST(s) were mapped for retro_mmus_2247 retrocopy.

TSS

No TSS is located nearby retro_mmus_2247 retrocopy 5' end.

Lab

retro_mmus_2247 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2247 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000023847	1 retrocopy	retro_btau_1752,
Cavia porcellus	ENSCPOG00000021914	1 retrocopy	retro_cpor_3,
Mus musculus	ENSMUSG00000040167	1 retrocopy	retro_mmus_2247 ,
Oryctolagus cuniculus	ENSOCUG00000013340	1 retrocopy	retro_ocun_935,