RetrogeneDB ID: retro_mmul_1032

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 13:74869191..74869813(-)
• Located in intron of: ENSMMUG00000002140

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.2525
• Ensembl ID: ENSMMUG00000019203
• Aliases: TVP23B, FAM18B, FAM18B1
• Description: None

Sequence

>retro_mmul_1032
ATGAAGCAGTAGGATAGTAATGATGACACTGCAGATGTTTCACTATTTGATACAGAAGAGGAGACAACTGATAGACCAAA
AAAATCCAAAAATCAGATATTCAGTGGTATCATTTTTCCACTTATTCTTTCAAGTCAGTCTACCTTCATTCATCATCTGT
CTTCTCTATGAGTTACTCAGCAGCAGCTTTATTGCCTGTATGATGACAATTATCTTGTTGTTGTCATGTGACTTTTGGGC
AGCAAAGAATGTCACAGGTAGACTAACGGTTGGTCTATGTTGGTGGTGTCACATAGATGAAGATGGAAAGAGCCATTGGG
TGTTTGAATCTAGAAAGGCGTCCTCTCAAGAGAATAAAACTGTGTCAGAAGCTGAATCAAGAATCTTTTGATTGGGACTT
ATAGCCTGTGCAGTGCTTTGGGTGATATTTGCCTTTAGTGCCCTGTTCTCCTTCAGGGTAAACTGGTTAGCAGTGGTTAT
TATGGGTATAGTGCTACCAGATGCCAACCTATATGGTTACATCAGGTGTAAGGTGAGCAGCAGAAAGAATTTAACCAACA
TGGCTACCTTGTATCTTGTAAAGCAGTTTTTAAGACAAAACACTGGAGATGATCAGAGAAGC

Alignment

ORF - retro_mmul_1032 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.73 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLQQDSNDDTEDVSLFDAEEETTNRPRKSK-IRHPVASFFHLFFRVS--AIVVYLLCELLSSSFITCMVT
          M.Q.DSNDDT.DVSLFD.EEETT.RP.KSK.IR..V.SFFHLFF.VS.......LL.ELLSSSFI.CM.T
Retrocopy MKQ*DSNDDTADVSLFDTEEETTDRPKKSK>IRYSVVSFFHLFFQVSLPSFIICLLYELLSSSFIACMMT

Parental  IILLLSCDFWAVKNVTGRLMVGLRWWNHIDEDGKSHWVFESRKESSQENKTVSEAESRIFWLGLIACPVL
          IILLLSCDFWA.KNVTGRL.VGL.WW.HIDEDGKSHWVFESRK.SSQENKTVSEAESRIF.LGLIAC.VL
Retrocopy IILLLSCDFWAAKNVTGRLTVGLCWWCHIDEDGKSHWVFESRKASSQENKTVSEAESRIF*LGLIACAVL

Parental  WVIFAFSALFSFRVKWLAVVIMGVVLQGANLYGYIRCKVGSRKNLTSMATSYFGKQFLRQNTGDDQTS
          WVIFAFSALFSFRV.WLAVVIMG.VL..ANLYGYIRCKV.SRKNLT.MAT.Y..KQFLRQNTGDDQ.S
Retrocopy WVIFAFSALFSFRVNWLAVVIMGIVLPDANLYGYIRCKVSSRKNLTNMATLYLVKQFLRQNTGDDQRS

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	21.51 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	15.39 RPM
SRP007412_cerebellum	0.00 RPM	26.93 RPM
SRP007412_heart	0.00 RPM	14.31 RPM
SRP007412_kidney	0.00 RPM	20.77 RPM
SRP007412_liver	0.00 RPM	12.23 RPM
SRP007412_testis	0.00 RPM	22.39 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1032 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1032 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1032 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2278

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005330	1 retrocopy	retro_cpor_184,
Dasypus novemcinctus	ENSDNOG00000007609	2 retrocopies	retro_dnov_1041, retro_dnov_1390,
Loxodonta africana	ENSLAFG00000003854	1 retrocopy	retro_lafr_465,
Microcebus murinus	ENSMICG00000015098	4 retrocopies	retro_mmur_1331, retro_mmur_151, retro_mmur_161, retro_mmur_683,
Myotis lucifugus	ENSMLUG00000002825	1 retrocopy	retro_mluc_1484,
Macaca mulatta	ENSMMUG00000019203	5 retrocopies	retro_mmul_1032 , retro_mmul_2125, retro_mmul_278, retro_mmul_600, retro_mmul_748,
Nomascus leucogenys	ENSNLEG00000014658	2 retrocopies	retro_nleu_1961, retro_nleu_2008,
Oryctolagus cuniculus	ENSOCUG00000000498	1 retrocopy	retro_ocun_759,
Otolemur garnettii	ENSOGAG00000012225	1 retrocopy	retro_ogar_978,
Rattus norvegicus	ENSRNOG00000050649	1 retrocopy	retro_rnor_636,
Ictidomys tridecemlineatus	ENSSTOG00000000642	6 retrocopies	retro_itri_1415, retro_itri_1841, retro_itri_310, retro_itri_473, retro_itri_711, retro_itri_782,
Tarsius syrichta	ENSTSYG00000008082	2 retrocopies	retro_tsyr_2000, retro_tsyr_530,