RetrogeneDB ID: retro_mmul_62

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 18:55547045..55548377(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000002207
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: COPS2
• Ensembl ID: ENSMMUG00000009838
• Aliases: None
• Description: COP9 signalosome complex subunit 2 [Source:RefSeq peptide;Acc:NP_001180530]

Sequence

>retro_mmul_62
ATGTCTGACATGGAGGATGATTTCACGTGCGATGATGAGGAGGACTACGACCTGGAATACTCTGAAGATAGTAACTCCGA
GCCAAATGTGGATTTGGAAAATCAGTACTATAATTCCAAAGCATTAAAAGAAGATGACTCAAAAGCAGCGTTAAGCAGTT
TCCAAAAGGTTTTGGAACTTGAAGGTGAAAAAGGAGAATGGGGATTTAAAGCACTGAAACAAATGATTAAGATTAACTCC
AAGTTGACAAACTTTCCAGAAATGATGAATAGATATAAACAGCTATTGACCTATATTCGGAGTGCAGTCACAAGAAATTA
TTCTGAAAAATCCATTAATTCTATTCTTGATTATATCTCTACTTCTAAACAGATGGATTTACTGCAGGAATTCTATGAAA
CAACACTGGAAGCTTTGAAAGATGCTAAGAATGATAGACTGTGGTTTAAGACAAACACAAAGCTTGGAAAATTATATTTA
GAACGAGAGGAATATGGAAAGCTTCAAAAAATTTTACACCAGTTACATCAGTCCTGCCAGACTGATGATGGAGAAGATGA
TCTGAAAAAAGGTACACAGTTATTAGAAATATATGCTTTGGAAATTCAAATGTACACAGCACAGAAAAATAACAAAAAAC
TTAAAGCACTCTATGAACAGTCACTTCACATCAAGTCTGCCATCCCTCATCCACTGATTATGGGAGTTATCAGAGAATGT
GGTGGTAAAATGCACTTGAGAGAAGGTGAATTTGAAAAGGCACACACTGATTTTTTTGAAGCCTTCAAGAATTATGATGA
ATCTGGAAGTCCAAGACGAACCACTTGCTTAAAATATTTGGTCTTAGCAAATATGCTTATGAAATCGGGAATAAATCCAT
TTGACTCACAGGAGGCCAAGCCGTACAAAAATGATCCAGAAATTTTAGCAATGACGAATTTAGTAAGTGCCTATCAGAAT
AATGACATCACTGAATTTGAAAAGATTCTAAAAACAAATCACAGCAACATCATGGATGATCCTTTCATAAGAGAACACAT
CGAAGAGCTTTTGCGAAACATCAGAACACAAGTGCTTATAAAATTAATTAAGCCTTACACAAGAATACATATTCCTTTTA
TTTCTAAGGAGTTAAACATAGATGTAGCTGATGTGGAGAGCTTGCTGGTGCAGTGCATATTGGATAACACTATTCATGGC
CGAACTGATCAAGTCAACCAACTCCTTGAACTGGATCATCAGAAGAGGGGTGGTGCACGATATACTGCACTAGATAAATG
GAGCAACCAACTAAATTCTCTCAACCAGGCTGTAGTCAGTAAACTGGCTTAA

Alignment

ORF - retro_mmul_62 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.14 %
• Parental protein coverage: 71.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QMDLLQEFYETTLEALKDAKNDRLWFKTNTKLGKLYLEREEYGKLQKILRQLHQSCQTDDGEDDLKKGTQ
          QMDLLQEFYETTLEALKDAKNDRLWFKTNTKLGKLYLEREEYGKLQKIL.QLHQSCQTDDGEDDLKKGTQ
Retrocopy QMDLLQEFYETTLEALKDAKNDRLWFKTNTKLGKLYLEREEYGKLQKILHQLHQSCQTDDGEDDLKKGTQ

Parental  LLEIYALEIQMYTAQKNNKKLKALYEQSLHIKSAIPHPLIMGVIRGKFECGGKMHLREGEFEKAHTDFFE
          LLEIYALEIQMYTAQKNNKKLKALYEQSLHIKSAIPHPLIMGVIR...ECGGKMHLREGEFEKAHTDFFE
Retrocopy LLEIYALEIQMYTAQKNNKKLKALYEQSLHIKSAIPHPLIMGVIR---ECGGKMHLREGEFEKAHTDFFE

Parental  AFKNYDESGSPRRTTCLKYLVLANMLMKSGINPFDSQEAKPYKNDPEILAMTNLVSAYQNNDITEFEKIL
          AFKNYDESGSPRRTTCLKYLVLANMLMKSGINPFDSQEAKPYKNDPEILAMTNLVSAYQNNDITEFEKIL
Retrocopy AFKNYDESGSPRRTTCLKYLVLANMLMKSGINPFDSQEAKPYKNDPEILAMTNLVSAYQNNDITEFEKIL

Parental  KTNHSNIMDDPFIREHIEELLRNIRTQVLIKLIKPYTRIHIPFISKELNIDVADVESLLVQCILDNTIHG
          KTNHSNIMDDPFIREHIEELLRNIRTQVLIKLIKPYTRIHIPFISKELNIDVADVESLLVQCILDNTIHG
Retrocopy KTNHSNIMDDPFIREHIEELLRNIRTQVLIKLIKPYTRIHIPFISKELNIDVADVESLLVQCILDNTIHG

Parental  RIDQVNQLLELDHQKRGGARYTALDKWTNQLNSLNQAVVSKLA
          R.DQVNQLLELDHQKRGGARYTALDKW.NQLNSLNQAVVSKLA
Retrocopy RTDQVNQLLELDHQKRGGARYTALDKWSNQLNSLNQAVVSKLA

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	1.90 RPM	17.82 RPM
SRP007412_brain_prefrontal_cortex	2.54 RPM	19.91 RPM
SRP007412_cerebellum	1.23 RPM	17.31 RPM
SRP007412_heart	0.47 RPM	15.31 RPM
SRP007412_kidney	0.70 RPM	15.84 RPM
SRP007412_liver	0.36 RPM	7.16 RPM
SRP007412_testis	1.24 RPM	12.29 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_62 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_62 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_62 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013425	1 retrocopy	retro_btau_452,
Choloepus hoffmanni	ENSCHOG00000013375	7 retrocopies	retro_chof_1083, retro_chof_1288, retro_chof_2209, retro_chof_2371, retro_chof_2520, retro_chof_2550, retro_chof_678,
Callithrix jacchus	ENSCJAG00000001585	2 retrocopies	retro_cjac_3105, retro_cjac_3117,
Echinops telfairi	ENSETEG00000019523	2 retrocopies	retro_etel_2160, retro_etel_88,
Macaca mulatta	ENSMMUG00000009838	1 retrocopy	retro_mmul_62 ,
Monodelphis domestica	ENSMODG00000002466	1 retrocopy	retro_mdom_891,
Oryctolagus cuniculus	ENSOCUG00000006455	1 retrocopy	retro_ocun_1296,
Otolemur garnettii	ENSOGAG00000013284	1 retrocopy	retro_ogar_1513,
Tupaia belangeri	ENSTBEG00000008306	1 retrocopy	retro_tbel_4497,
Tursiops truncatus	ENSTTRG00000000462	1 retrocopy	retro_ttru_328,