RetrogeneDB ID: retro_mmus_1920

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:54240568..54241312(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082096
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Zcchc9
• Ensembl ID: ENSMUSG00000021621
• Aliases: Zcchc9, 1810019C21Rik
• Description: zinc finger, CCHC domain containing 9 [Source:MGI Symbol;Acc:MGI:1916335]

Sequence

>retro_mmus_1920
ATGACCAGGTGGACTAGAGTTACTACTTCAGATAGTAAGAGACCCCTGTCAACAACATCATCGGAGGCTATGAAGAAGGG
ATCTGCCGAGAGAGTAGAACAAAACCTGGCAAACCATAAGCAACGTCAACGCAGTGGGCTGTCCCTTAGAAATGATTCAC
CTCAAGCTAAACGCAAAAAGAACAAAAAGAAGAAAAGAGTACTTGAGTGAAGATGTGAATGGATTCATGGAGTACCTAAA
ACAGAACTCACAGGTGCTTCACAATGGACAGTTGATAGCAGCCGACAGCCTGGAAGTAAGGGAAGAACTTGCAGTGGCCT
AAAAGAAGGGCAGTTGACCGGAATGAAGGTGGCTAAAGAGACAGGCAGCAAAGAAGACTTCAATGGTATGTTCCCATTGT
CAACAACCTAGCTATGGAATTGCTGACTGCTCAGCCATACTAGAGAGTCAGGACATGGACACCGGCATTCGTTGCTGCTG
CGGGTCCACGGAGCACGAGATGACGAAGCGCAGAGCTAACGAAGACCCTGCACTTGGTGAATTTCCTTTTGAAAATGTTT
TGTTTGTGGAGAAATGGGACGCCTCTCCAGATCCTGCCCTGATAATACCAAAGGAGTCTATGCTGATGGTGGCGGCTGTA
AACTCTGTGGCTCCGTGGAACCTTTTAAGAAAGACTGCCCTGAAAATCAGAACTCAGATCAGATCATCACAGTTGGTCGC
TGGGCAAATGGAATGAGTGCAGAC

Alignment

ORF - retro_mmus_1920 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.8 %
• Parental protein coverage: 91.51 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MTRWARVTTSNSKRPLSATSWEDMKKGSVERADQSLPNRKQCQSSRLPLRNDSPQAKRKKNKKKK-EYLN
          MTRW.RVTTS.SKRPLS.TS.E.MKKGS.ER..Q.L.N.KQ.Q.S.L.LRNDSPQAKRKKNKKKK.EYL.
Retrocopy MTRWTRVTTSDSKRPLSTTSSEAMKKGSAERVEQNLANHKQRQRSGLSLRNDSPQAKRKKNKKKK>EYLS

Parental  EDVNGFMEYLKQNSQVLHNGQLIAADSQEVREEIAVALKKDSRREGRRLKRQAAKKNAMVCFHCRQPGHG
          EDVNGFMEYLKQNSQVLHNGQLIAADS.EVREE.AVA.KK.S..E.R.LKRQAAKK..MVC.HC.QP..G
Retrocopy EDVNGFMEYLKQNSQVLHNGQLIAADSLEVREELAVA*KKGS*PE*RWLKRQAAKKTSMVCSHCQQPSYG

Parental  IADCPAVLESQDMGTGICYRCGSTEHEMSKCRANVDPALGEFPFA-KCFVCGEMGHLSRSCPDNTKGVYA
          IADC.A.LESQDM.TGI...CGSTEHEM.K.RAN.DPALGEFPF..KCFVCGEMG.LSRSCPDNTKGVYA
Retrocopy IADCSAILESQDMDTGIRCCCGSTEHEMTKRRANEDPALGEFPFE<KCFVCGEMGRLSRSCPDNTKGVYA

Parental  DGGSCKLCGSVEHFKKDCRENQNSDRIITVGRWAKGMSAD
          DGG.CKLCGSVE.FKKDC.ENQNSD.IITVGRWA.GMSAD
Retrocopy DGGGCKLCGSVEPFKKDCPENQNSDQIITVGRWANGMSAD

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	0.00 RPM	12.17 RPM
SRP007412_cerebellum	0.00 RPM	14.37 RPM
SRP007412_heart	0.00 RPM	11.46 RPM
SRP007412_kidney	0.00 RPM	19.31 RPM
SRP007412_liver	0.00 RPM	10.27 RPM
SRP007412_testis	0.27 RPM	4.76 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1920 was not detected

EST

No EST(s) were mapped for retro_mmus_1920 retrocopy.

TSS

No TSS is located nearby retro_mmus_1920 retrocopy 5' end.

Lab

retro_mmus_1920 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1920 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 40 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005265	1 retrocopy	retro_btau_1095,
Canis familiaris	ENSCAFG00000008703	2 retrocopies	retro_cfam_1547, retro_cfam_675,
Choloepus hoffmanni	ENSCHOG00000005268	3 retrocopies	retro_chof_140, retro_chof_2143, retro_chof_268,
Callithrix jacchus	ENSCJAG00000019486	4 retrocopies	retro_cjac_1236, retro_cjac_2906, retro_cjac_3528, retro_cjac_909,
Echinops telfairi	ENSETEG00000003838	2 retrocopies	retro_etel_325, retro_etel_880,
Homo sapiens	ENSG00000131732	1 retrocopy	retro_hsap_1799,
Gorilla gorilla	ENSGGOG00000013790	1 retrocopy	retro_ggor_706,
Microcebus murinus	ENSMICG00000016266	5 retrocopies	retro_mmur_125, retro_mmur_1325, retro_mmur_1341, retro_mmur_606, retro_mmur_819,
Myotis lucifugus	ENSMLUG00000001886	1 retrocopy	retro_mluc_799,
Macaca mulatta	ENSMMUG00000020655	1 retrocopy	retro_mmul_797,
Mus musculus	ENSMUSG00000021621	1 retrocopy	retro_mmus_1920 ,
Otolemur garnettii	ENSOGAG00000002543	6 retrocopies	retro_ogar_1467, retro_ogar_2125, retro_ogar_2426, retro_ogar_2941, retro_ogar_3076, retro_ogar_459,
Pongo abelii	ENSPPYG00000015604	1 retrocopy	retro_pabe_1476,
Pan troglodytes	ENSPTRG00000017047	2 retrocopies	retro_ptro_1205, retro_ptro_602,
Rattus norvegicus	ENSRNOG00000014927	2 retrocopies	retro_rnor_1164, retro_rnor_2160,
Sorex araneus	ENSSARG00000008580	2 retrocopies	retro_sara_216, retro_sara_78,
Sarcophilus harrisii	ENSSHAG00000014504	1 retrocopy	retro_shar_734,
Ictidomys tridecemlineatus	ENSSTOG00000001407	2 retrocopies	retro_itri_422, retro_itri_696,
Tarsius syrichta	ENSTSYG00000012423	1 retrocopy	retro_tsyr_244,
Tursiops truncatus	ENSTTRG00000013796	1 retrocopy	retro_ttru_819,