RetrogeneDB ID: retro_mmus_2572

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:60674293..60675229(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Pogk
• Ensembl ID: ENSMUSG00000040596
• Aliases: Pogk, 9130401E23Rik, BASS2, mKIAA1513
• Description: pogo transposable element with KRAB domain [Source:MGI Symbol;Acc:MGI:1918842]

Sequence

>retro_mmus_2572
ATGAATCTGGAACATCCAGAAATGGAGTTCTGAGCCTACCCTCTAAATTTGACCCTGAAAGAAGAGCAAAAGGAAGAAGA
GATTGAGATCCAGGAATTGGAGGATGGACCCATAGATATTCAGAAAGTACAAATCTGCTCGGAAACTGCATGGGTACCAG
TCCTATTTGATGAGGTGGCCATATATTTTTCGGAGGAAGATTGGGAAGTTCTGACAGAGCAACAAAAATCCCTCTACCGG
GAAGTCATGAGGATGAATTATGAGACTGTCCTGTCCCTGGAATTCCCATTCCCCAGGACAGAAATGATCAATTGGGTGGA
AAGGAAAGAGCAGTGTCCTAATTCTGATGAGTGGCGGCTCCAGGGAGTAATCTTTGCAGAAAATGAAGAATCTGACCTAG
GACTCCAGATTGGGCAAGCCCGATGAATGCCACCTCCCATTTTCCTCAACCTCTTCAACAGCTTTCGACTGTGTCTGCCT
CAGAACATCACTGAACTGCCTGAGTGGAGTGAGGGCTACCCTTTCTATACAGCCATGGGCTTCCCTGGGTATGACCTCTC
AGCTGACGTCGAAGTGAGCTAATTTCAGTTCAGTTGTAGCATGTGCCTCAGTTATGATGCAGGGTTCACGCTGATCATGG
TAGAGTATGCAGAGCCCACCAACAACTGTCAGGCTGCCAATCCGTTTGGGGTGTTAGAAAAAAATGTTTGAGACTAGAGC
AAAGTGAAGCCACAGCTGCAAAATGCTCATACCATGTGGCGAGCATTCCAAGGTCGCAAGAAATGAAGGTTTGCTGTGGT
AGACCAGCGAGTGTCTGAGGATGTCAGATACATACTGGCCAAAGGGGACCCCATCACTAGGGAGGAAATGCAGTTGAAAG
CTCTTGAAATCGCCCAGGAAATGAACATTCCAGAGGAAGGGTTCAAGGCAAGAATG

Alignment

ORF - retro_mmus_2572 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.7 %
• Parental protein coverage: 51.14 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MNLENPEMESRAYPLNLTLKEEQKEEEVEIQELEDGPIDMQKVQICSEGAWVPALFDEVAIYFSDEEWEV
          MNLE.PEME..AYPLNLTLKEEQKEEE.EIQELEDGPID.QKVQICSE.AWVP.LFDEVAIYFS.E.WEV
Retrocopy MNLEHPEMEF*AYPLNLTLKEEQKEEEIEIQELEDGPIDIQKVQICSETAWVPVLFDEVAIYFSEEDWEV

Parental  LTEQQKALYREVMRMNYETVLSLEFPFPKPDMINRLERDEECPNSDEWRLQGVTFAENEESDF-RTPDWA
          LTEQQK.LYREVMRMNYETVLSLEFPFP...MIN..ER.E.CPNSDEWRLQGV.FAENEESD..RTPDWA
Retrocopy LTEQQKSLYREVMRMNYETVLSLEFPFPRTEMINWVERKEQCPNSDEWRLQGVIFAENEESDL<RTPDWA

Parental  SPTNATSHFPQPQP-FNSFGLRLPQDITELPEWTEGYPFYMAMGFPGYDLSADDLASKFQFSRGMRRSYD
          SP.NATSHFP..QP.FNSF.L.LPQ.ITELPEW.EGYPFY.AMGFPGYDLSAD...S.FQFS..M..SYD
Retrocopy SPMNATSHFP--QP>FNSFRLCLPQNITELPEWSEGYPFYTAMGFPGYDLSADVEVS*FQFSCSMCLSYD

Parental  AGFKLMVVEYAESTNNCQAAKQFGVLEKNVRDWRKVKPQLQNAHAMRRAFRGPKNGRFALVDQRVAEYVR
          AGF.L..VEYAE.TNNCQAA..FGVLEKNV.D..KVKPQLQNAH.M.RAF.G.K..RFA.VDQRV.E.VR
Retrocopy AGFTLIMVEYAEPTNNCQAANPFGVLEKNV*D*SKVKPQLQNAHTMWRAFQGRKK*RFAVVDQRVSEDVR

Parental  YMQAKGDPITREAMQLKALEIAQEMNIPEKGFKASL
          Y..AKGDPITRE.MQLKALEIAQEMNIPE.GFKA..
Retrocopy YILAKGDPITREEMQLKALEIAQEMNIPEEGFKARM

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	0.02 RPM	76.28 RPM
SRP007412_cerebellum	0.00 RPM	94.62 RPM
SRP007412_heart	0.00 RPM	25.65 RPM
SRP007412_kidney	0.02 RPM	31.99 RPM
SRP007412_liver	0.00 RPM	10.76 RPM
SRP007412_testis	0.00 RPM	29.18 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2572 was not detected

EST

No EST(s) were mapped for retro_mmus_2572 retrocopy.

TSS

No TSS is located nearby retro_mmus_2572 retrocopy 5' end.

Lab

retro_mmus_2572 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2572 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000033914	1 retrocopy	retro_cjac_2779,
Dipodomys ordii	ENSDORG00000006822	1 retrocopy	retro_dord_612,
Erinaceus europaeus	ENSEEUG00000014393	1 retrocopy	retro_eeur_21,
Latimeria chalumnae	ENSLACG00000014539	1 retrocopy	retro_lcha_56,
Mus musculus	ENSMUSG00000040596	1 retrocopy	retro_mmus_2572 ,
Otolemur garnettii	ENSOGAG00000007615	1 retrocopy	retro_ogar_2784,
Tarsius syrichta	ENSTSYG00000011078	1 retrocopy	retro_tsyr_1983,