RetrogeneDB ID: retro_mmus_770

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 11:22758694..22759549(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000084081
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Metap2
• Ensembl ID: ENSMUSG00000036112
• Aliases: Metap2, 4930584B20Rik, A930035J23Rik, AI047573, AL024412, AU014659, Amp2, Mnpep, p67, p67eIF2
• Description: methionine aminopeptidase 2 [Source:MGI Symbol;Acc:MGI:1929701]

Sequence

>retro_mmus_770
GAGATTTGGAACAACCTCCAAGAAGCTACAGAAGCACATCAGCAAGTTAGGAGATACATCATGAGCTGGATCAAGCCTGC
AATGGCGATGATGGAAATCTGTAAAAAGTTAGATGACCGTTCCTGAAAGCTAATAAAGGAAAATGGGTTAAATGCAGGCC
TGGAATTTCCCACCGGGTGTTCTCTCAACAACTGTGCTGCACATAACACTCCTAACGCTGGTGACACAACAGTCTTACAG
TACAATGACATCTGTAAGATAGACTTTGGGACACTTATAAGTGGTAGAATAATTGATTGTGCTTTTACTGTTACTTTTAA
TCCCAGATATGACACATTATTTAAAGCTGTAGAAGATGCCATTACTTCTGGTATAAAGTGTGCTGGGATTGACGTCTGTC
TCTGTGATGTTGAGGAGGCTATTCAAGAAGTTATGCAATCCTATGAAGTAGAAATAGATGGGAAGACATATCAAGTGAAA
CCCATACATAACTTAAATGGACATTCAATTGGGCCATATAGAATTCATGCTGGAAAAACAGTGCCCATTATGAAAGGCAG
GGAAGCTACAAGAATGGAGGAAGAAGAGGTGTATGCCATTGAGACCTCTGGGAGCACAGGGAAGGGTGTGGTTCATGATG
ACATGGAAGGTTCACACTACATGAAAAAGTTTGATGTGGGACATGTGCCAGTAAGGCTTCCAAGAACAAAACACTCATTA
AATGTCATCAATGAAAACTTTGGTACCCTTGCCTTCTGCCGAAGGTGGCTGGATCGCTTGGGAGAAAGTAAATACTTAAT
TGCTCTGAAGAATCTATGTGACTTGGAGATTGTAGATCCATACCTACCACTGTGC

Alignment

ORF - retro_mmus_770 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.61 %
• Parental protein coverage: 58.4 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EIWNDFREAAEAHRQVRKYVMSWIKPGMTMIEICEKLEDCSRKLIKENGLNAGLAFPTGCSLNNCAAHYT
          EIWN...EA.EAH.QVR.Y.MSWIKP.M.M.EIC.KL.D.S.KLIKENGLNAGL.FPTGCSLNNCAAH.T
Retrocopy EIWNNLQEATEAHQQVRRYIMSWIKPAMAMMEICKKLDDRS*KLIKENGLNAGLEFPTGCSLNNCAAHNT

Parental  PNAGDTTVLQYDDICKIDFGTHISGRIIDCAFTVTFNPKYDILLTAVKDATNTGIKCAGIDVRLCDVGEA
          PNAGDTTVLQY.DICKIDFGT.ISGRIIDCAFTVTFNP.YD.L..AV.DA...GIKCAGIDV.LCDV.EA
Retrocopy PNAGDTTVLQYNDICKIDFGTLISGRIIDCAFTVTFNPRYDTLFKAVEDAITSGIKCAGIDVCLCDVEEA

Parental  IQEVMESYEVEIDGKTYQVKPIRNLNGHSIGPYRIHAGKTVPIVKGGEATRMEEGEVYAIETFGSTGKGV
          IQEVM.SYEVEIDGKTYQVKPI.NLNGHSIGPYRIHAGKTVPI.KG.EATRMEE.EVYAIET.GSTGKGV
Retrocopy IQEVMQSYEVEIDGKTYQVKPIHNLNGHSIGPYRIHAGKTVPIMKGREATRMEEEEVYAIETSGSTGKGV

Parental  VHDDMECSHYMKNFDVGHVPIRLPRTKHLLNVINENFGTLAFCRRWLDRLGESKYLMALKNLCDLGIVDP
          VHDDME.SHYMK.FDVGHVP.RLPRTKH.LNVINENFGTLAFCRRWLDRLGESKYL.ALKNLCDL.IVDP
Retrocopy VHDDMEGSHYMKKFDVGHVPVRLPRTKHSLNVINENFGTLAFCRRWLDRLGESKYLIALKNLCDLEIVDP

Parental  YPPLC
          Y.PLC
Retrocopy YLPLC

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	0.19 RPM	69.71 RPM
SRP007412_cerebellum	0.09 RPM	82.24 RPM
SRP007412_heart	0.00 RPM	92.36 RPM
SRP007412_kidney	0.15 RPM	119.85 RPM
SRP007412_liver	0.03 RPM	60.71 RPM
SRP007412_testis	1.14 RPM	207.06 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_770 was not detected

EST

No EST(s) were mapped for retro_mmus_770 retrocopy.

TSS

No TSS is located nearby retro_mmus_770 retrocopy 5' end.

Lab

retro_mmus_770 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_770 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000006353	1 retrocopy	retro_cfam_1330,
Monodelphis domestica	ENSMODG00000008173	1 retrocopy	retro_mdom_297,
Mus musculus	ENSMUSG00000025364	1 retrocopy	retro_mmus_2803,
Mus musculus	ENSMUSG00000036112	2 retrocopies	retro_mmus_3689, retro_mmus_770 ,
Otolemur garnettii	ENSOGAG00000008469	1 retrocopy	retro_ogar_2163,
Rattus norvegicus	ENSRNOG00000021881	2 retrocopies	retro_rnor_1707, retro_rnor_547,