RetrogeneDB ID: retro_mmus_945

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 12:69675663..69676314(-)
• Located in intron of: ENSMUSG00000034801

Retrocopy information

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

Parental gene information

• Parental gene symbol: Clic4
• Ensembl ID: ENSMUSG00000037242
• Aliases: Clic4, D0Jmb3, TU-74, mc3s5, mtCLIC
• Description: chloride intracellular channel 4 (mitochondrial) [Source:MGI Symbol;Acc:MGI:1352754]

Sequence

>retro_mmus_945
ATGGCACTGTCGATGGCCTTGAAAGGGCTGAAGGAGGAGGAAAAGAGCCCCTCATCCAGCTCTCCATCAAGGCGGGCAGA
TGGAGAAAGCATAGGACACCACCCCCTTTCACAGGGGTGCTTCATGATTCTTAGGCTCAAAGGAGCCATGTTTAGTGTCA
CAACCACTGGATTCAAAAGGAAACCTGTGAACCTGCAGAGCTTGACTCCAGGAATCCACACACCATTTATAACTTTCAAC
AGTGAGGTCAAAACAGATGTAAATAAGATTGAGGAATCTCTTGAACAAGTCTTATCCAGCCTACCCCACCAAGTACTTAA
ATCTTTCACCAAAACCCCCAGAGTCAAACACGGCTGGAACGTCTTGTCAGTTTCTCTGCTTATATCAAGACCTCAAGGCC
AGAGGCTAATGAACCACTGGAGAGGGGGCTCCTAAAAATGCTGCAGGAACTAGAGGAGCTGAGTTCCCCCCTCTCTCATG
ACGTTGGTGAGAACAGCAAGGAGGACATGGAGCTTTCCACATGTAGATTTCTGGACGGCAATGAGATGATATTAGTGGAC
TGCCTGGCACCTGCAGCCAAGCACCTTGTCTAGGTGGTGGCCAGCAAATCCCACCACTTTGATATTCTAAAGGACTGACG
GCATCTGGAGA

Alignment

ORF - retro_mmus_945 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.48 %
• Parental protein coverage: 86.56 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MALSMPLNGLKEEDKEPLIELFVKAGSDGESIGNCPFSQRLFMILWLKGVVFSVTTVDLKRKPADLQNLA
          MALSM.L.GLK.E..............DGESIG..P.SQ..FMIL.LKG..FSVTT...KRKP..LQ.L.
Retrocopy MALSMALKGLK-EEEKSPSSSSPSRRADGESIGHHPLSQGCFMILRLKGAMFSVTTTGFKRKPVNLQSLT

Parental  PGTHPPFITFNSEVKTDVNKIEEFLEEVLC--PPKYLKLSPK-HPESNTAGMDIFAKFSAYIKNSRPEAN
          PG.H.PFITFNSEVKTDVNKIEE.LE.VL...P...LK...K..P.S.T........FSAYIK.SRPEAN
Retrocopy PGIHTPFITFNSEVKTDVNKIEESLEQVLSSLPHQVLKSFTK<NPQSQTR-LERLVSFSAYIKTSRPEAN

Parental  EALERGLLKTLQKLDEYLNSPLPDEIDENSMEDIKFSTRRFLDGDEMTLADCNLLPKLHIVKVVAKKYRN
          E.LERGLLK.LQ.L.E.L.SPL.....ENS.ED...ST.RFLDG.EM.L.DC......H.V.VVA.K...
Retrocopy EPLERGLLKMLQELEE-LSSPLSHDVGENSKEDMELSTCRFLDGNEMILVDCLAPAAKHLV*VVASKSHH

Parental  FDI-PKGMT-GIWR
          FDI..KG.T.GIWR
Retrocopy FDI<SKGLT<GIWR

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	89.01 RPM
SRP007412_cerebellum	0.04 RPM	96.22 RPM
SRP007412_heart	0.03 RPM	346.54 RPM
SRP007412_kidney	0.10 RPM	246.99 RPM
SRP007412_liver	0.03 RPM	73.16 RPM
SRP007412_testis	0.00 RPM	63.67 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_945 was not detected

EST

No EST(s) were mapped for retro_mmus_945 retrocopy.

TSS

No TSS is located nearby retro_mmus_945 retrocopy 5' end.

Lab

retro_mmus_945 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_945 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007591	10 retrocopies	retro_chof_1284, retro_chof_1401, retro_chof_1446, retro_chof_1654, retro_chof_2177, retro_chof_2673, retro_chof_784, retro_chof_789, retro_chof_808, retro_chof_947,
Callithrix jacchus	ENSCJAG00000020833	2 retrocopies	retro_cjac_1713, retro_cjac_461,
Cavia porcellus	ENSCPOG00000004010	1 retrocopy	retro_cpor_1490,
Homo sapiens	ENSG00000169504	2 retrocopies	retro_hsap_4143, retro_hsap_4678,
Gorilla gorilla	ENSGGOG00000005586	2 retrocopies	retro_ggor_1579, retro_ggor_2783,
Macropus eugenii	ENSMEUG00000008789	1 retrocopy	retro_meug_780,
Macaca mulatta	ENSMMUG00000002416	2 retrocopies	retro_mmul_1183, retro_mmul_2488,
Mus musculus	ENSMUSG00000037242	2 retrocopies	retro_mmus_2259, retro_mmus_945 ,
Nomascus leucogenys	ENSNLEG00000008997	3 retrocopies	retro_nleu_1457, retro_nleu_1785, retro_nleu_2168,
Otolemur garnettii	ENSOGAG00000014620	1 retrocopy	retro_ogar_2672,
Pongo abelii	ENSPPYG00000001715	3 retrocopies	retro_pabe_219, retro_pabe_3466, retro_pabe_3632,
Pan troglodytes	ENSPTRG00000000350	3 retrocopies	retro_ptro_2816, retro_ptro_3107, retro_ptro_396,
Pteropus vampyrus	ENSPVAG00000005838	1 retrocopy	retro_pvam_812,
Ictidomys tridecemlineatus	ENSSTOG00000002184	1 retrocopy	retro_itri_52,
Tarsius syrichta	ENSTSYG00000008978	1 retrocopy	retro_tsyr_252,
Vicugna pacos	ENSVPAG00000007699	1 retrocopy	retro_vpac_475,