RetrogeneDB ID: retro_mmus_1262

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 14:32266975..32267589(-)
• Located in intron of: ENSMUSG00000021911

Retrocopy information

• Ensembl ID: ENSMUSG00000091570
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Emc2
• Ensembl ID: ENSMUSG00000022337
• Aliases: Emc2, 4921531G14Rik, AV060620, AW209495, Ttc35
• Description: ER membrane protein complex subunit 2 [Source:MGI Symbol;Acc:MGI:1913986]

Sequence

>retro_mmus_1262
GTGACGATTGCAGTCCTAGACTAAGGTCGGGATGACTTGGCATTGTTTTGTCTTCAGGACTTAAGAAGACAATTCCCTGG
CAGTCACAGAGTTAAACAATTAACAAGCATTCGATTTGAAGCTATGGAAAGATATGACGATGCTATACAACTGTATGATC
GAATTTTGCAAGAAGATCCAACTAACACTGCTGCCAGAAAGCGTAAGATTGCCATTCAAAAAGCCCAGGGGAAAAACGTG
GAGGCCACTGGAGAGCTGGATGAGTATCTGGAACAGTTTGCTGGAGACCAAGAAGCCCGGCATGAACCTGCAGAACTTTG
TATCAATGAACATGACTATGCCAAAGTAGCCGTTTGCTTAGAGGAGCTGATGATGACAAATCCACATAACCACGTATACT
GTCAACAGTATGTAGAAATCAAATACACCCAAGGTGGACTTGAAAACGTCGAGGTTTCAAGAAAGTATTTTGCACAGGCA
CTGAACCTAAACAATAGAAACATGAGAGCTCTGTTTGGCCTTTACATGTCTGCAAATCATACTGCTTCTAATCCAAAAGC
AAGTGCAAAAATGAAAAAGGCAACATCAAATATGCTAGTTAGGTTGCTAATCAA

Alignment

ORF - retro_mmus_1262 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.44 %
• Parental protein coverage: 69.02 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VMIAALDYGRDDLALFCLQELRRQFPGSHRVKRLTGMRFEAMERYDDAIQLYDRILQEDPTNTAARKRKI
          V.IA.LD.GRDDLALFCLQ.LRRQFPGSHRVK.LT..RFEAMERYDDAIQLYDRILQEDPTNTAARKRKI
Retrocopy VTIAVLD*GRDDLALFCLQDLRRQFPGSHRVKQLTSIRFEAMERYDDAIQLYDRILQEDPTNTAARKRKI

Parental  AIRKAQGKTVEAIRELNEYLEQFVGDQEAWHELAELYINEHDYAKAAFCLEELMMTNPHNHLYCQQYAEV
          AI.KAQGK.VEA..EL.EYLEQF.GDQEA.HE.AEL.INEHDYAK.A.CLEELMMTNPHNH.YCQQY.E.
Retrocopy AIQKAQGKNVEATGELDEYLEQFAGDQEARHEPAELCINEHDYAKVAVCLEELMMTNPHNHVYCQQYVEI

Parental  KYTQGGLENLELSRKYFAQALKLNNRNMRALFGLYMSASHIASNPKASAKMK-KDNIKYASWAANQ
          KYTQGGLEN.E.SRKYFAQAL.LNNRNMRALFGLYMSA.H.ASNPKASAKMK.K.NIKYAS..ANQ
Retrocopy KYTQGGLENVEVSRKYFAQALNLNNRNMRALFGLYMSANHTASNPKASAKMK<KGNIKYAS*VANQ

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	39.81 RPM
SRP007412_cerebellum	0.04 RPM	32.00 RPM
SRP007412_heart	0.06 RPM	61.64 RPM
SRP007412_kidney	0.02 RPM	48.78 RPM
SRP007412_liver	0.00 RPM	25.04 RPM
SRP007412_testis	0.00 RPM	32.89 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1262 was not detected

EST

No EST(s) were mapped for retro_mmus_1262 retrocopy.

TSS

No TSS is located nearby retro_mmus_1262 retrocopy 5' end.

Lab

retro_mmus_1262 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1262 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012826	1 retrocopy	retro_amel_600,
Canis familiaris	ENSCAFG00000000713	1 retrocopy	retro_cfam_726,
Choloepus hoffmanni	ENSCHOG00000011271	3 retrocopies	retro_chof_1512, retro_chof_1990, retro_chof_851,
Callithrix jacchus	ENSCJAG00000006437	2 retrocopies	retro_cjac_3295, retro_cjac_3867,
Myotis lucifugus	ENSMLUG00000013258	2 retrocopies	retro_mluc_2369, retro_mluc_2452,
Mustela putorius furo	ENSMPUG00000005915	1 retrocopy	retro_mputfur_1647,
Mus musculus	ENSMUSG00000022337	1 retrocopy	retro_mmus_1262 ,
Oryctolagus cuniculus	ENSOCUG00000002461	1 retrocopy	retro_ocun_1251,
Pongo abelii	ENSPPYG00000018820	1 retrocopy	retro_pabe_1600,