RetrogeneDB ID: retro_mmul_135

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 2:58866738..58867866(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000009425
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: MMU.17389
• Ensembl ID: ENSMMUG00000011153
• Aliases: None
• Description: actin, cytoplasmic 1 [Source:RefSeq peptide;Acc:NP_001028256]

Sequence

>retro_mmul_135
ATGGATGATGATATCGCCGCGCTCGTTGTCGACAACGGCTCCGGCATGTGCAAGGCCGGCTTCGCGGGCGACGATGCCCC
CCGGGCCGTCTTCCCCTCCATCGTGGGGCGCCCCAGGCACCAGGGCGTGATGGTGGGCATGGGTCAGAAGGATTCATATG
TGGGCGACGAGGCCCAGAGCAAGAGAGGCATTCTCACCCTGAAGTACCCCATCGAGCACGGCATCGTCACCAACTGGGAC
GACATGGAGAAGATCTGGCACCACACCTTCTACAATGAGCTGCGTGTGGCTCCTGAGGAGCACCCCGTGCTGCTGACCGA
GGCCCCCCTGAACCCCAAGGCCAACCGCGAGAAGATGACCCAGATCATGTTTGAGACCTTCAACACCCCAGCCATGTACG
TGGCCATCCAGGCTGTGCTGTCCCTGTACGCCTCTGGCCGTACCACTGGCATCGTGATGGACTCCGGTGACGGGGTCACC
CACACTGTGCCCATCTACGAGGGGTATGCCCTCCCCCATGCCATCCTGCGTCTGGACCTGGCTGGCCGGGACCTGACTGA
CTACCTCATGAAGATCCTCACTGAGCGCGGCTACAGCTTCACCACCACGGCCGAGCGGGAAATCGTGCGTGACATTAAGG
AGAAGCTGTGCTATGTCGCCCTAGACTTCGAGCAGGAGATGGCCACGGCGGCTTCCAGCTCCTCCCTGGAGAAGAGCTAC
GAGCTGCCCGATGGCCAGGTCATCACCATTGGCAACGAGCGGTTCCGCTGCCCTGAGGCTCTCTTCCAACCTTCCTTCCT
GGGCATGGAGTCCTGTGGCATCCACGAAACTACCTTCAACTCCATCATGAAGTGTGACGTGGACATCCGTAAAGACCTGT
ACGCCAACACAGTGCTGTCTGGTGGCACCACCATGTACCCTGGCATTGCTGACAGGATGCAGAAGGAGATTACTGCCCTG
GCGCCCAGCACGATGAAGATCAAGATCATTGCTCCTCCTGAGCGCAAGTACTCTGTGTGGATCGGCGGCTCCATCCTGGC
CTCGCTGTCCACCTTCCAGCAGATGTGGATCAGCAAGCAGGAGTATGACGAGTCTGGCCCTTCCATCGTCCACCGCAAAT
GCTTCTAG

Alignment

ORF - retro_mmul_135 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

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

Retrocopy - Parental Gene Alignment:

Parental  MDDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYP
          MDDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYP
Retrocopy MDDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYP

Parental  IEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVL
          IEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVL
Retrocopy IEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVL

Parental  SLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVR
          SLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVR
Retrocopy SLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVR

Parental  DIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFN
          DIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFN
Retrocopy DIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFN

Parental  SIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLS
          SIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLS
Retrocopy SIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLS

Parental  TFQQMWISKQEYDESGPSIVHRKCF
          TFQQMWISKQEYDESGPSIVHRKCF
Retrocopy TFQQMWISKQEYDESGPSIVHRKCF

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	78.10 RPM	78.44 RPM
SRP007412_brain_prefrontal_cortex	137.00 RPM	904.76 RPM
SRP007412_cerebellum	49.08 RPM	56.70 RPM
SRP007412_heart	43.22 RPM	68.54 RPM
SRP007412_kidney	87.09 RPM	87.79 RPM
SRP007412_liver	189.88 RPM	290.35 RPM
SRP007412_testis	17.11 RPM	34.45 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

5 EST(s) were mapped to retro_mmul_135 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BQ807588	58866671	58867201	99.9	529	1	528
BQ807667	58866664	58867148	99.8	482	1	480
CN641765	58866934	58867367	97.6	409	5	392
CO582814	58866665	58867191	98.7	516	6	505
CO648223	58866908	58867376	97.3	454	12	439

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_135 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_135 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 27 parental genes, and 125 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006601	1 retrocopy	retro_amel_11,
Anas platyrhynchos	ENSAPLG00000010147	1 retrocopy	retro_apla_2,
Canis familiaris	ENSCAFG00000016020	3 retrocopies	retro_cfam_120, retro_cfam_260, retro_cfam_934,
Callithrix jacchus	ENSCJAG00000000008	2 retrocopies	retro_cjac_243, retro_cjac_56,
Cavia porcellus	ENSCPOG00000013467	1 retrocopy	retro_cpor_60,
Dipodomys ordii	ENSDORG00000010079	1 retrocopy	retro_dord_11,
Equus caballus	ENSECAG00000015935	2 retrocopies	retro_ecab_271, retro_ecab_994,
Felis catus	ENSFCAG00000006788	1 retrocopy	retro_fcat_1613,
Homo sapiens	ENSG00000075624	6 retrocopies	retro_hsap_1563, retro_hsap_1894, retro_hsap_3386, retro_hsap_38, retro_hsap_4204, retro_hsap_518,
Gallus gallus	ENSGALG00000009621	1 retrocopy	retro_ggal_4,
Gorilla gorilla	ENSGGOG00000001133	18 retrocopies	retro_ggor_1177, retro_ggor_1188, retro_ggor_1211, retro_ggor_1266, retro_ggor_1297, retro_ggor_1332, retro_ggor_1387, retro_ggor_1622, retro_ggor_1825, retro_ggor_1890, retro_ggor_2292, retro_ggor_2774, retro_ggor_2817, retro_ggor_3002, retro_ggor_352, retro_ggor_405, retro_ggor_44, retro_ggor_477,
Loxodonta africana	ENSLAFG00000009167	1 retrocopy	retro_lafr_116,
Meleagris gallopavo	ENSMGAG00000003960	2 retrocopies	retro_mgal_5, retro_mgal_6,
Macaca mulatta	ENSMMUG00000011153	1 retrocopy	retro_mmul_135 ,
Mustela putorius furo	ENSMPUG00000016612	2 retrocopies	retro_mputfur_440, retro_mputfur_461,
Mus musculus	ENSMUSG00000029580	7 retrocopies	retro_mmus_1613, retro_mmus_1677, retro_mmus_283, retro_mmus_2880, retro_mmus_3411, retro_mmus_3532, retro_mmus_761,
Ornithorhynchus anatinus	ENSOANG00000007716	2 retrocopies	retro_oana_4, retro_oana_8,
Otolemur garnettii	ENSOGAG00000008348	1 retrocopy	retro_ogar_2637,
Petromyzon marinus	ENSPMAG00000004161	1 retrocopy	retro_pmar_4,
Pongo abelii	ENSPPYG00000017336	23 retrocopies	retro_pabe_1281, retro_pabe_1292, retro_pabe_1575, retro_pabe_1610, retro_pabe_1772, retro_pabe_1816, retro_pabe_1911, retro_pabe_2042, retro_pabe_2168, retro_pabe_2175, retro_pabe_2188, retro_pabe_227, retro_pabe_2754, retro_pabe_2811, retro_pabe_2824, retro_pabe_2862, retro_pabe_2978, retro_pabe_309, retro_pabe_3563, retro_pabe_3567, retro_pabe_3746, retro_pabe_745, retro_pabe_86,
Pan troglodytes	ENSPTRG00000018890	27 retrocopies	retro_ptro_1042, retro_ptro_1051, retro_ptro_1076, retro_ptro_1143, retro_ptro_1272, retro_ptro_1515, retro_ptro_1756, retro_ptro_178, retro_ptro_2122, retro_ptro_2173, retro_ptro_2349, retro_ptro_2454, retro_ptro_263, retro_ptro_2805, retro_ptro_2854, retro_ptro_314, retro_ptro_3207, retro_ptro_3219, retro_ptro_3282, retro_ptro_3287, retro_ptro_3292, retro_ptro_3302, retro_ptro_3307, retro_ptro_387, retro_ptro_432, retro_ptro_53, retro_ptro_584,
Rattus norvegicus	ENSRNOG00000034254	10 retrocopies	retro_rnor_1324, retro_rnor_1386, retro_rnor_1799, retro_rnor_2371, retro_rnor_2714, retro_rnor_2856, retro_rnor_2978, retro_rnor_351, retro_rnor_459, retro_rnor_935,
Sarcophilus harrisii	ENSSHAG00000012694	4 retrocopies	retro_shar_120, retro_shar_370, retro_shar_62, retro_shar_93,
Sus scrofa	ENSSSCG00000007585	1 retrocopy	retro_sscr_548,
Ictidomys tridecemlineatus	ENSSTOG00000006868	2 retrocopies	retro_itri_1675, retro_itri_531,
Ictidomys tridecemlineatus	ENSSTOG00000014797	3 retrocopies	retro_itri_149, retro_itri_1881, retro_itri_4,
Xenopus tropicalis	ENSXETG00000025116	1 retrocopy	retro_xtro_6,