RetrogeneDB ID: retro_mmul_1770

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:67884760..67885940(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000022289
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MMU.3260
• Ensembl ID: ENSMMUG00000018653
• Aliases: None
• Description: None

Sequence

>retro_mmul_1770
ACTTCCTACTGCTACAGCCAGTCGTCCGCAAAGTCGTCCTTCGGGGGCCTGGGCGGCGGCTCCGTGAGTTTGGGGCCAGG
GGTCGCCTTTTGCGCGCCCAGCATGCACTGGGGCCGGCGGCCGCGGCGCTTCCGTGTCCTCCGCCGCTTCGTGTCTGTTC
TCGTCCTCCTTGGGGGGCTACAGCGGCGTCCTGGCCGCGTCCGACCGGCTGCTGGAGGGCAACGAGAAGCTCACTATGCA
GAACCTCAACGACCGCCTGGCCTCCTACCTGGACAAGGTGCGCGCCCTGGAGGCTGCCAACTGCGAGCTGGAGGTGAAGA
TCCGCGACTGGTACCAGAAGCAGGGTCCCGGGCCCTCCCGTGACTACAGCCACTACTACAAGACCATCCAGGACCTGCAG
GACAAGCTTCTTGGTGCCACCATTGAGAACTCCAGGATTGTCCTGGAGATCGACAACGCCCATCTGGCTGCAGATAACTT
CCGAACCAAGACTGACACGGAGCAGGCTCTGCGCATGACCGTGGAGGCCGACATCAACGGCCTGCACAGGGTGCTGGACG
AGCTGACCCTGGCCAGTACCGACCTGGAGATGCAGATTGAAGGCCTGAAGGAAGAGCTGGCCCACCTGAAGAAGAACCAT
GAAGAGGAAATCAGTGGGCTGAGGGGCCAAGTGGGAGGCCAGGTCAGTGTGGAGGTGGATTCTGCTCGGGGCACCGATCT
CGCCAGGATCTTGAGTGGCATGCGAAGCCAATACAAGGTCATGGCGGAGCAGAACTGGAAGGATGCTGAAGCCTGGTTCA
CCAGCCGGACTGAAGAATTGAACCGAGAGGTCGCTGGCCACACGGATCAGCTCCACATGAGCCTGTCCAAGGTGACTGAC
CTGCAGCGCACCCTCCAGGGTCTTGAGCTGCAGTCACAGCTGAGCATGAAAGCCACCTTGGAAGGCACACTGGCAGAAAC
GGAGGCGCGCGTTGGAGCCCAGCTGGCGCAGATCCAGTCGCTGATCAACGGTATTGAAGCCCAGCTGGGCGATGTGCGAG
CTGATAGTGAGCGGCAGAATCAGGAGTACCAGCAGTTCACGGACAACAAGTCGCGGCTGCAGCAGGAGATCGCCACCTAC
CGCAGCCTGCTCGAGGGCCGGGAAGATCACTACAATAATCTTTCTGCCTCCAAGGTCCTC

Alignment

ORF - retro_mmul_1770 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.25 %
• Parental protein coverage: 99.75 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TSYSYRQSSATSSFGGLGGGSVRFGPGVAFRAPSMH-GGSGGRGVSVSSARFVSSSSSGGYGGGYGGVLA
          TSY.Y.QSSA.SSFGGLGGGSV..GPGVAF.APSMH.G..G.RG.SVSSA.....SSS.G...GY.GVLA
Retrocopy TSYCYSQSSAKSSFGGLGGGSVSLGPGVAFCAPSMH>GAGG-RGASVSSAASCLFSSSLG---GYSGVLA

Parental  ASDGLLAGNEKLTMQNLNDRLASYLDKVRALEAANGELEVKIRDWYQKQGPGPSRDYSHYYTTIQDLRDK
          ASD.LL.GNEKLTMQNLNDRLASYLDKVRALEAAN.ELEVKIRDWYQKQGPGPSRDYSHYY.TIQDL.DK
Retrocopy ASDRLLEGNEKLTMQNLNDRLASYLDKVRALEAANCELEVKIRDWYQKQGPGPSRDYSHYYKTIQDLQDK

Parental  ILGATIENSRIVLQIDNARLAADDFRTKFETEQALRMSVEADINGLRRVLDELTLARTDLEMQIEGLKEE
          .LGATIENSRIVL.IDNA.LAAD.FRTK..TEQALRM.VEADINGL.RVLDELTLA.TDLEMQIEGLKEE
Retrocopy LLGATIENSRIVLEIDNAHLAADNFRTKTDTEQALRMTVEADINGLHRVLDELTLASTDLEMQIEGLKEE

Parental  LAYLKKNHEEEISVLRGQVGGQVSVEVDSAPGTDLAKILSDMRSQYEVMAEQNRKDAEAWFTSRTEELNR
          LA.LKKNHEEEIS.LRGQVGGQVSVEVDSA.GTDLA.ILS.MRSQY.VMAEQN.KDAEAWFTSRTEELNR
Retrocopy LAHLKKNHEEEISGLRGQVGGQVSVEVDSARGTDLARILSGMRSQYKVMAEQNWKDAEAWFTSRTEELNR

Parental  EVAGHTEQLQISRSEVTDLRRTLQGLEIELQSQLSMKAALEDTLAETEARFGAQLAHIQALISGVEAQLG
          EVAGHT.QL..S.S.VTDL.RTLQGL..ELQSQLSMKA.LE.TLAETEAR.GAQLA.IQ.LI.G.EAQLG
Retrocopy EVAGHTDQLHMSLSKVTDLQRTLQGL--ELQSQLSMKATLEGTLAETEARVGAQLAQIQSLINGIEAQLG

Parental  DVRADSERQNQEYQRLMDIKSRLEQEIATYRSLLEGQEDHYNNLSASKVL
          DVRADSERQNQEYQ...D.KSRL.QEIATYRSLLEG.EDHYNNLSASKVL
Retrocopy DVRADSERQNQEYQQFTDNKSRLQQEIATYRSLLEGREDHYNNLSASKVL

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	0.11 RPM	1.79 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	2.54 RPM
SRP007412_cerebellum	0.06 RPM	0.39 RPM
SRP007412_heart	0.00 RPM	15.07 RPM
SRP007412_kidney	0.23 RPM	10.33 RPM
SRP007412_liver	0.00 RPM	0.99 RPM
SRP007412_testis	83.57 RPM	1.24 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1770 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1770 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1770 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3486
Pan troglodytes	retro_ptro_2359
Gorilla gorilla	retro_ggor_2352
Pongo abelii	retro_pabe_2880

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000029756	9 retrocopies	retro_cjac_1151, retro_cjac_1812, retro_cjac_2347, retro_cjac_2646, retro_cjac_3108, retro_cjac_3198, retro_cjac_3237, retro_cjac_3358, retro_cjac_633,
Equus caballus	ENSECAG00000014086	2 retrocopies	retro_ecab_76, retro_ecab_931,
Echinops telfairi	ENSETEG00000007881	6 retrocopies	retro_etel_1217, retro_etel_1319, retro_etel_191, retro_etel_480, retro_etel_685, retro_etel_95,
Homo sapiens	ENSG00000171345	3 retrocopies	retro_hsap_3486, retro_hsap_585, retro_hsap_959,
Gorilla gorilla	ENSGGOG00000016901	3 retrocopies	retro_ggor_2352, retro_ggor_518, retro_ggor_773,
Macropus eugenii	ENSMEUG00000016158	3 retrocopies	retro_meug_1860, retro_meug_403, retro_meug_826,
Macaca mulatta	ENSMMUG00000018653	4 retrocopies	retro_mmul_1770 , retro_mmul_717, retro_mmul_774, retro_mmul_790,
Nomascus leucogenys	ENSNLEG00000010787	3 retrocopies	retro_nleu_1609, retro_nleu_2204, retro_nleu_800,
Oryctolagus cuniculus	ENSOCUG00000016132	1 retrocopy	retro_ocun_1884,
Otolemur garnettii	ENSOGAG00000024306	1 retrocopy	retro_ogar_1301,
Ochotona princeps	ENSOPRG00000007908	2 retrocopies	retro_opri_337, retro_opri_673,
Pongo abelii	ENSPPYG00000008416	3 retrocopies	retro_pabe_2880, retro_pabe_603, retro_pabe_820,
Pan troglodytes	ENSPTRG00000009168	3 retrocopies	retro_ptro_2074, retro_ptro_2359, retro_ptro_430,
Ictidomys tridecemlineatus	ENSSTOG00000014403	2 retrocopies	retro_itri_1514, retro_itri_697,