RetrogeneDB ID: retro_mmus_2988

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:7061870..7062688(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Pafah1b1
• Ensembl ID: ENSMUSG00000020745
• Aliases: Pafah1b1, LIS-1, Lis1, MMS10-U, Mdsh, Ms10u, Pafaha
• Description: platelet-activating factor acetylhydrolase, isoform 1b, subunit 1 [Source:MGI Symbol;Acc:MGI:109520]

Sequence

>retro_mmus_2988
GTTACTCAGGTCAATTTCCATCCTGTGTTCAGCATTATGGTCTCTGCTTCAGATGATGCTACAATTAAGATGTGGGATTA
TAAGACTGGAGATTTTGAGCAAACTCTCAAGGGCCATACAGACTCTGTACAGGACATTTCCTTTGACCACAGTGGCAAGC
TTTTGGCTTTCTGTTCTGCAGATATGATGATTAAATTATGGGATTTTCAGGGTTTTGAGTGCATCAGAACCATGCATGGC
CATGACCACAGTGTCTCTTCAGTAGCCATTATGCCTATTGGAAATTATATAGTGTCTGCCTCAAGGGATAAAACTATAAA
AATTTGGGAAGTGCAAACTGGCTACTGTGTGAAGACATTCATAGTATACAGAGAATGGGTATGGATGCTGCGGCCAAATC
AGGATGGCAGTCTGATAGCCAGCTGTTCCAATGACCAGACTGTGCGTGTGTGGGTTGTAGCAACAAAGGAATGCAAGGCT
GAGCTCCAAGAACATGCACATGTGGTGGAATGCATTTCCTGGGCTCCAGAAAGTTCATATTCTTCCATCTCTGAACCAAC
AAGATATGAGACTAAAATAAGTGACAAGTCTGGACCCTTCTTGCTATCTGGTTCCAGAGACAAAACTATTAAGATGTGGG
ATGTCAGTACTGGCATGTGCCTTATGACTCTTGTGGGCCATGATAATTAGGGACTTGGAGTTCTGATCAGGGTCAGAGGG
AGTTAATTTTGAATTGTGCTAATGACAAAACCCTCTGTGTATGCAAGTACAAGAACAAGGGAAGCATGAAGACCCTCAAT
GTGCATGAACACATTGTT

Alignment

ORF - retro_mmus_2988 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.85 %
• Parental protein coverage: 66.59 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VTRVIFHPVFSVMVSASEDATIKVWDYETGDFERTLKGHTDSVQDISFDHSGKLLASCSADMTIKLWDFQ
          VT.V.FHPVFS.MVSAS.DATIK.WDY.TGDFE.TLKGHTDSVQDISFDHSGKLLA.CSADM.IKLWDFQ
Retrocopy VTQVNFHPVFSIMVSASDDATIKMWDYKTGDFEQTLKGHTDSVQDISFDHSGKLLAFCSADMMIKLWDFQ

Parental  GFECIRTMHGHDHNVSSVAIMPNGDHIVSASRDKTIKMWEVQTGYCVKTFTGHREWVRMVRPNQDGTLIA
          GFECIRTMHGHDH.VSSVAIMP.G..IVSASRDKTIK.WEVQTGYCVKTF...REWV.M.RPNQDG.LIA
Retrocopy GFECIRTMHGHDHSVSSVAIMPIGNYIVSASRDKTIKIWEVQTGYCVKTFIVYREWVWMLRPNQDGSLIA

Parental  SCSNDQTVRVWVVATKECKAELREHEHVVECISWAPESSYSSISEATGSETKKSGKPGPFLLSGSRDKTI
          SCSNDQTVRVWVVATKECKAEL.EH.HVVECISWAPESSYSSISE.T..ETK.S.K.GPFLLSGSRDKTI
Retrocopy SCSNDQTVRVWVVATKECKAELQEHAHVVECISWAPESSYSSISEPTRYETKISDKSGPFLLSGSRDKTI

Parental  KMWDVSTGMCLMTLVGHDNWVRGVLFHSGG-KFILSCADDKTLRVWDYKNKRCMKTLNAHEHFV
          KMWDVSTGMCLMTLVGHDN...GVL....G...IL.CA.DKTL.V..YKNK..MKTLN.HEH.V
Retrocopy KMWDVSTGMCLMTLVGHDN*GLGVLIRVRG<ELILNCANDKTLCVCKYKNKGSMKTLNVHEHIV

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	584.66 RPM
SRP007412_cerebellum	0.04 RPM	498.30 RPM
SRP007412_heart	0.06 RPM	222.43 RPM
SRP007412_kidney	0.06 RPM	204.08 RPM
SRP007412_liver	0.05 RPM	85.83 RPM
SRP007412_testis	0.05 RPM	302.29 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2988 was not detected

EST

No EST(s) were mapped for retro_mmus_2988 retrocopy.

TSS

No TSS is located nearby retro_mmus_2988 retrocopy 5' end.

Lab

retro_mmus_2988 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2988 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000007168	2 retrocopies	retro_hsap_2144, retro_hsap_2292,
Monodelphis domestica	ENSMODG00000010776	2 retrocopies	retro_mdom_441, retro_mdom_460,
Mus musculus	ENSMUSG00000020745	1 retrocopy	retro_mmus_2988 ,
Mus musculus	ENSMUSG00000026917	1 retrocopy	retro_mmus_132,
Pongo abelii	ENSPPYG00000007796	1 retrocopy	retro_pabe_1932,
Pan troglodytes	ENSPTRG00000008551	1 retrocopy	retro_ptro_1569,
Sorex araneus	ENSSARG00000002826	4 retrocopies	retro_sara_266, retro_sara_275, retro_sara_364, retro_sara_588,