RetrogeneDB ID: retro_mmus_2978

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:136657341..136658070(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BC005624
• Ensembl ID: ENSMUSG00000026851
• Aliases: None
• Description: cDNA sequence BC005624 [Source:MGI Symbol;Acc:MGI:2385132]

Sequence

>retro_mmus_2978
ATGGGTGTGGCTGCCCTGCTGATAGGAGAGAAGGTTCAAGAGGAGACTACTCTGGTGGATGATCCCTTCCAAATGGCGAC
AGGGGTCATGGTGGACATGAAGAAACTGAAGGAGCAGGGCAAAGACAAGGTCAGTGAAGAGGAGGATCTGCACCTGGGGA
CATCGTTTGCTGCAGAGACCAACCGGAGGGACGAAGATGCAGACATGATGAAGTACATTGAGACGGGGCTGAAGAAGAGG
AAGGGGATTGTGGAGCAAGAGGAACAGAAGGCCAAGCCCAAGAATGCTGAGGACTGCCCCTATGAGCTGCCAGAGAATAT
CCGAGTCTCTTCTGCCAAGAAGACTGAGGAGATGCTGTCCAACCAGATGCTGAGTGGCATCCCTGAGGTGGACCTGGGCA
TAGACGCTAAAATAAAAAACATCATTTCCACAGAGGATGCCAAGGCCCAGCTGCTGGCAGAGCAGCAGAACAAGAAGAAG
GATAGCGAGACATCTTTTGTGCCCACCAACATGGCTGTGAACTATGTGCAGCACAACCGATTTTATCACGAGGAGCTCGA
TGCACCCATCCGAAGAAACAAAGAAGAGCCCAGAGCCCGGCCCTTGCGAGTGGGTGACACAGAAAAGCCAGAGCCTGAAC
GGTCCCCTCCCAACCGCAAGCGTCCTGCTAATGAAAAGGCCACAGATGACTACCACTATGAGAAGTTCAAGAAGATGAAC
AGGCGCTAC

Alignment

ORF - retro_mmus_2978 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.06 %
• Parental protein coverage: 84.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VSAAALLVGEKVQEETTLVDDPFQMATGGMVDMKKLKERGKDKVSEEEDLHLGTSFSAETNRRDEDADMM
          ...AALL.GEKVQEETTLVDDPFQMATG.MVDMKKLKE.GKDKVSEEEDLHLGTSF.AETNRRDEDADMM
Retrocopy MGVAALLIGEKVQEETTLVDDPFQMATGVMVDMKKLKEQGKDKVSEEEDLHLGTSFAAETNRRDEDADMM

Parental  KYIETELKKRKGIVEQEEQKAKPKNAEDCLYELPENIRVSSAKKTEEMLSNQMLSGIPEVDLGIDAKIKN
          KYIET.LKKRKGIVEQEEQKAKPKNAEDC.YELPENIRVSSAKKTEEMLSNQMLSGIPEVDLGIDAKIKN
Retrocopy KYIETGLKKRKGIVEQEEQKAKPKNAEDCPYELPENIRVSSAKKTEEMLSNQMLSGIPEVDLGIDAKIKN

Parental  IISTEDAKARLLAEQQNKKKDSETSFVPTNMAVNYVQHNRFYHEELNAPIRRNKEEPKARPLRVGDTEKP
          IISTEDAKA.LLAEQQNKKKDSETSFVPTNMAVNYVQHNRFYHEEL.APIRRNKEEP.ARPLRVGDTEKP
Retrocopy IISTEDAKAQLLAEQQNKKKDSETSFVPTNMAVNYVQHNRFYHEELDAPIRRNKEEPRARPLRVGDTEKP

Parental  EPERSPPNRKRPANEKATDDYHYEKFKKMNRRY
          EPERSPPNRKRPANEKATDDYHYEKFKKMNRRY
Retrocopy EPERSPPNRKRPANEKATDDYHYEKFKKMNRRY

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	0.09 RPM	43.01 RPM
SRP007412_cerebellum	0.04 RPM	66.48 RPM
SRP007412_heart	0.16 RPM	26.15 RPM
SRP007412_kidney	0.13 RPM	41.31 RPM
SRP007412_liver	0.00 RPM	28.07 RPM
SRP007412_testis	0.09 RPM	40.89 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2978 was not detected

EST

No EST(s) were mapped for retro_mmus_2978 retrocopy.

TSS

No TSS is located nearby retro_mmus_2978 retrocopy 5' end.

Lab

retro_mmus_2978 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2978 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020307	1 retrocopy	retro_btau_1138,
Canis familiaris	ENSCAFG00000019979	1 retrocopy	retro_cfam_116,
Choloepus hoffmanni	ENSCHOG00000013895	3 retrocopies	retro_chof_1103, retro_chof_1747, retro_chof_978,
Cavia porcellus	ENSCPOG00000009285	1 retrocopy	retro_cpor_712,
Equus caballus	ENSECAG00000018958	1 retrocopy	retro_ecab_174,
Gorilla gorilla	ENSGGOG00000013358	1 retrocopy	retro_ggor_1990,
Macropus eugenii	ENSMEUG00000010524	3 retrocopies	retro_meug_1046, retro_meug_1241, retro_meug_508,
Microcebus murinus	ENSMICG00000009596	1 retrocopy	retro_mmur_1466,
Monodelphis domestica	ENSMODG00000006832	1 retrocopy	retro_mdom_518,
Mus musculus	ENSMUSG00000026851	1 retrocopy	retro_mmus_2978 ,
Otolemur garnettii	ENSOGAG00000009770	1 retrocopy	retro_ogar_1015,
Pongo abelii	ENSPPYG00000019685	1 retrocopy	retro_pabe_2426,
Sarcophilus harrisii	ENSSHAG00000012313	1 retrocopy	retro_shar_746,
Ictidomys tridecemlineatus	ENSSTOG00000020630	1 retrocopy	retro_itri_1783,
Tupaia belangeri	ENSTBEG00000013115	1 retrocopy	retro_tbel_514,