RetrogeneDB ID: retro_mmul_2488

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:38834250..38835006(+)
• 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_2488
ATGGCGTTGTCGATGCCGCTGAACCGGCTGAAGGAGGAGAACAAAGAGCCCCTCATTGAGCACCTCGTCAAAGCTGGCAG
TGATGGTGAAAGCATAGGAAACTGCCCCTTTTCCCAGAGGCTCTTCATGATTCATTGACTCAAAGGAGTTGTATTTAGTG
TCACAACTGTTGACCTGAAAAGGAAGCCTGCAGACCTTCAGAACTTAGCTCCCGGGACCCACCCACCATTTATAAGTTTC
AACAGTGAAGTCAAAACGGATGTAAGTAAGATTGAGGAATTTCTTGAAGAAGTCTTATGCCCTCCCAAGTACTTAAAGCT
TTCACCAAAACACCCAGAATCAAATACTGCTGGAATGGACATCTTTGCCAAATTCTCTGCATTTATCAAGAATTGAAGGC
GAGAGGCTAATGAAGCACTGGAGAAGGATCTCCTAAAAACTCTGCAGAAACTGGATAAATATCTGAATTCTCCTCTCCCT
GATGAAACTGATGAAAATAGTATAGAGGACATTAAGTTTTCTACACGTAAATTTCTGGATGGCAACGAAATGACATTAGC
TAATTGCAACCTGCTGCCCAAACTGCATATTGTCAAGGTGGTGGCCAAAAAATATTACAACTTTGATATTCCAAAAGAGA
TGACTGGCATCTGGAGATACCTAACTAATGCATACAGTAGGGACGAGTTCCTCAATACCTGTCCCAGTGATAAGGAGGTT
GAAATAGCTTATAGTGATGCCAAAAGACCCACCAAG

Alignment

ORF - retro_mmul_2488 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.3 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MALSMPLNGLKEEDKEPLIELFVKAGSDGESIGNCPFSQRLFMILWLKGVVFSVTTVDLKRKPADLQNLA
          MALSMPLN.LKEE.KEPLIE..VKAGSDGESIGNCPFSQRLFMI..LKGVVFSVTTVDLKRKPADLQNLA
Retrocopy MALSMPLNRLKEENKEPLIEHLVKAGSDGESIGNCPFSQRLFMIH*LKGVVFSVTTVDLKRKPADLQNLA

Parental  PGTHPPFITFNSEVKTDVNKIEEFLEEVLCPPKYLKLSPKHPESNTAGMDIFAKFSAYIKNSRPEANEAL
          PGTHPPFI.FNSEVKTDV.KIEEFLEEVLCPPKYLKLSPKHPESNTAGMDIFAKFSA.IKN.R.EANEAL
Retrocopy PGTHPPFISFNSEVKTDVSKIEEFLEEVLCPPKYLKLSPKHPESNTAGMDIFAKFSAFIKN*RREANEAL

Parental  ERGLLKTLQKLDEYLNSPLPDEIDENSMEDIKFSTRKFLDGNEMTLADCNLLPKLHIVKVVAKKYRNFDI
          E..LLKTLQKLD.YLNSPLPDE.DENS.EDIKFSTRKFLDGNEMTLA.CNLLPKLHIVKVVAKKY.NFDI
Retrocopy EKDLLKTLQKLDKYLNSPLPDETDENSIEDIKFSTRKFLDGNEMTLANCNLLPKLHIVKVVAKKYYNFDI

Parental  PKDMTGIWRYLTNAYSRDEFTNTCPSDKEVEIAYSDVAKRLTK
          PK.MTGIWRYLTNAYSRDEF.NTCPSDKEVEIAYSD.AKR.TK
Retrocopy PKEMTGIWRYLTNAYSRDEFLNTCPSDKEVEIAYSD-AKRPTK

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_2488 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2488 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2488 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4678
Pongo abelii	retro_pabe_3632

---

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,