RetrogeneDB ID: retro_mmul_1183

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 15:54329092..54329540(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.4332
• Ensembl ID: ENSMMUG00000002416
• Aliases: None
• Description: chloride intracellular channel protein 4 [Source:RefSeq peptide;Acc:NP_001248536]

Sequence

>retro_mmul_1183
GATAGTGGTGGAGTGTCTCCAAATTAAAGAGAAGGGAACATAACTTTCAACAGTGAAGTCAAAACTGATATAAATAAGAT
TGAGGCATTTATTGAAGTCTAAGCCCTCCCACATACTTCAAGCCTTCACCAAAACATCCAGAATCAAATACTGCTAGAAT
GGACATCTTTGCCAAATTCTCTGCATATATCAAGAATTCCAGGCCAGAGGCTAATGAAGTACTGGAGAGGGGTCTCCTGA
AAACCCTGCAGAAAACTGGATGAATATCTGAATTCTCCTCTCTCTGATGAAATTGATGAAAATACTATGGAGGACGTTAA
GTTTTCTAGACGTAAATTTCTAGAAAATGAAATGACATTAGCTGATTGCAACCTGCTGCCAAAACTGCATAGTGTCAAGG
TAGTGGCCAAAAAAATATCACAACTTTGATATTCCAGAAGAAATAACT

Alignment

ORF - retro_mmul_1183 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.27 %
• Parental protein coverage: 59.68 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DLQNLAPGTHPPFITFNSEVKTDVNKIEEFLEEV-LCPPKYLKLSPKHPESNTAGMDIFAKFSAYIKNSR
          D.....P......ITFNSEVKTD.NKIE.F..EV.L.PP.Y.K.SPKHPESNTA.MDIFAKFSAYIKNSR
Retrocopy DSGGVSPN*REGNITFNSEVKTDINKIEAFI-EV<LSPPTYFKPSPKHPESNTARMDIFAKFSAYIKNSR

Parental  PEANEALERGLLKTLQ-KLDEYLNSPLPDEIDENSMEDIKFSTRKFLDGNEMTLADCNLLPKLHIVKVVA
          PEANE.LERGLLKTLQ.KLDEYLNSPL.DEIDEN.MED.KFS.RKFL..NEMTLADCNLLPKLH.VKVVA
Retrocopy PEANEVLERGLLKTLQ>KLDEYLNSPLSDEIDENTMEDVKFSRRKFLE-NEMTLADCNLLPKLHSVKVVA

Parental  -KKYRNFDIPKDMT
          .KKY.NFDIP...T
Retrocopy >KKYHNFDIPEEIT

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	52.55 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	21.82 RPM
SRP007412_cerebellum	0.00 RPM	45.53 RPM
SRP007412_heart	0.00 RPM	195.21 RPM
SRP007412_kidney	0.12 RPM	293.07 RPM
SRP007412_liver	0.00 RPM	33.29 RPM
SRP007412_testis	0.00 RPM	35.51 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1183 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1183 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1183 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 39 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,
Macaca mulatta	ENSMMUG00000029827	3 retrocopies	retro_mmul_1269, retro_mmul_290, retro_mmul_902,
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,