RetrogeneDB ID: retro_mmul_11

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 7:26385477..26386218(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000016097
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMMUG00000021313
• Aliases: None
• Description: None

Sequence

>retro_mmul_11
ATGGCGGAGCAAGAGCAAAGAAAAATCCCTTTGGTTCCAGAAAATCTGCTGAAAAAGAGGAAGGCTTATCAAGCCCTCAA
AGCCACCCAGGCAAAGCAGGCACTTTTGGCAAAGAAGGAGCAGAGGAAAGGAAAAGGGCTCAGGTTTAAGCGACTGGAAT
CATTCCTACATGATTCCTGGCGGCAGAAACGTGACAAGGTGCGTCTCAGACGACTAGAAGTGAAACCTCATGCCTTGGAA
TTGCCAGACAAACATTCCTTGGCCTTTGTTGTACGCATCGAAAGGATTGATGGCGTGAGTTTATTGGTGCAGAGAACCAT
TGCAAGACTTCGCCTAAAGAAAATTTTTAGTGGTGTCTTTGTAAAAGTCACCCCCCAGAACCTAAAAATGCTGCGTATAG
TGGAACCTTATGTGACCTGGGGATTTCCAAATCTGAAGTCTGTCCGAGAACTCATTTTGAAACGTGGACAAGCCAAGGTC
AAGAATAAGACCATCCCTCTGACAGACAACACAGTGATTGAGGAGCACCTGGGGAAGTTTGGCGTCATTTGCTTGGAAGA
CCTCATTCATGAAATTGCCTTCCCAGGGAAGCATTTCCAGGAGATCTCATGGTTCTTGCGCCCTTTCCACCTCTCAGTGG
CCCGACATGCTACCAAAAATAGAGTGGGCTTCCTCAAGGAGATGGGCACACCTGGCTATCGGGGTGAACGCATCAATCAG
CTCATCCGCCAGCTGAACTAG

Alignment

ORF - retro_mmul_11 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.17 %
• Parental protein coverage: 97.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QRKIPLVPENLLKKRKAYQALKATQAKQALLAKKEQRKGKGLRFKRLESFLHDSWRQKRDKVRLRRLEVK
          QRKIPLVPENLLKKRKAYQALKATQAKQALLAKKEQRKGKGLRFKRLESFLHDSWRQKRDKVRLRRLEVK
Retrocopy QRKIPLVPENLLKKRKAYQALKATQAKQALLAKKEQRKGKGLRFKRLESFLHDSWRQKRDKVRLRRLEVK

Parental  PHALELPDKHSLAFVVRIERIDGVSLLVQRTIARLRLKKIFSGVFVKVTPQNLKMLRIVEPYVTWGFPNL
          PHALELPDKHSLAFVVRIERIDGVSLLVQRTIARLRLKKIFSGVFVKVTPQNLKMLRIVEPYVTWGFPNL
Retrocopy PHALELPDKHSLAFVVRIERIDGVSLLVQRTIARLRLKKIFSGVFVKVTPQNLKMLRIVEPYVTWGFPNL

Parental  KSVRELILKRGQAKVKNKTIPLTDNTVIEEHLGKFGVICLEDLIHEIAFPGKHFQEISWFC-PFHLSVAR
          KSVRELILKRGQAKVKNKTIPLTDNTVIEEHLGKFGVICLEDLIHEIAFPGKHFQEISWF..PFHLSVAR
Retrocopy KSVRELILKRGQAKVKNKTIPLTDNTVIEEHLGKFGVICLEDLIHEIAFPGKHFQEISWFLRPFHLSVAR

Parental  HATKNRVGFLKEMGTPGYRGERINQLIRQLN
          HATKNRVGFLKEMGTPGYRGERINQLIRQLN
Retrocopy HATKNRVGFLKEMGTPGYRGERINQLIRQLN

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	2.24 RPM	2.02 RPM
SRP007412_brain_prefrontal_cortex	8.88 RPM	6.03 RPM
SRP007412_cerebellum	1.94 RPM	2.20 RPM
SRP007412_heart	1.12 RPM	1.00 RPM
SRP007412_kidney	2.23 RPM	1.64 RPM
SRP007412_liver	1.31 RPM	1.27 RPM
SRP007412_testis	0.90 RPM	1.55 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_11 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_11 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_11 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 28 parental genes, and 110 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012791	2 retrocopies	retro_amel_1260, retro_amel_243,
Bos taurus	ENSBTAG00000018478	2 retrocopies	retro_btau_588, retro_btau_816,
Canis familiaris	ENSCAFG00000001728	4 retrocopies	retro_cfam_1180, retro_cfam_1464, retro_cfam_1638, retro_cfam_330,
Choloepus hoffmanni	ENSCHOG00000000306	4 retrocopies	retro_chof_1168, retro_chof_1404, retro_chof_388, retro_chof_478,
Cavia porcellus	ENSCPOG00000021189	2 retrocopies	retro_cpor_1134, retro_cpor_653,
Dasypus novemcinctus	ENSDNOG00000013485	1 retrocopy	retro_dnov_689,
Equus caballus	ENSECAG00000003113	1 retrocopy	retro_ecab_998,
Erinaceus europaeus	ENSEEUG00000010431	1 retrocopy	retro_eeur_90,
Echinops telfairi	ENSETEG00000002419	3 retrocopies	retro_etel_1151, retro_etel_1823, retro_etel_542,
Felis catus	ENSFCAG00000009707	1 retrocopy	retro_fcat_143,
Gorilla gorilla	ENSGGOG00000009958	15 retrocopies	retro_ggor_1009, retro_ggor_1013, retro_ggor_1253, retro_ggor_1261, retro_ggor_1904, retro_ggor_2099, retro_ggor_2108, retro_ggor_2113, retro_ggor_2162, retro_ggor_2282, retro_ggor_2457, retro_ggor_2524, retro_ggor_2591, retro_ggor_2659, retro_ggor_2973,
Macaca mulatta	ENSMMUG00000005141	1 retrocopy	retro_mmul_129,
Macaca mulatta	ENSMMUG00000021313	1 retrocopy	retro_mmul_11 ,
Monodelphis domestica	ENSMODG00000019028	1 retrocopy	retro_mdom_1708,
Mustela putorius furo	ENSMPUG00000013296	1 retrocopy	retro_mputfur_1577,
Mus musculus	ENSMUSG00000063888	4 retrocopies	retro_mmus_2359, retro_mmus_3172, retro_mmus_3626, retro_mmus_777,
Oryctolagus cuniculus	ENSOCUG00000003844	6 retrocopies	retro_ocun_1393, retro_ocun_1604, retro_ocun_1818, retro_ocun_278, retro_ocun_509, retro_ocun_598,
Otolemur garnettii	ENSOGAG00000012671	3 retrocopies	retro_ogar_1380, retro_ogar_3358, retro_ogar_3428,
Pongo abelii	ENSPPYG00000016619	21 retrocopies	retro_pabe_1064, retro_pabe_1069, retro_pabe_1315, retro_pabe_1341, retro_pabe_1370, retro_pabe_1379, retro_pabe_1457, retro_pabe_2078, retro_pabe_2154, retro_pabe_2354, retro_pabe_2527, retro_pabe_2543, retro_pabe_2598, retro_pabe_2609, retro_pabe_2644, retro_pabe_2988, retro_pabe_3053, retro_pabe_3259, retro_pabe_3410, retro_pabe_3714, retro_pabe_3753,
Pteropus vampyrus	ENSPVAG00000008696	3 retrocopies	retro_pvam_1179, retro_pvam_1482, retro_pvam_975,
Rattus norvegicus	ENSRNOG00000016269	1 retrocopy	retro_rnor_2795,
Sorex araneus	ENSSARG00000005286	2 retrocopies	retro_sara_100, retro_sara_211,
Sarcophilus harrisii	ENSSHAG00000011219	1 retrocopy	retro_shar_216,
Sus scrofa	ENSSSCG00000026472	3 retrocopies	retro_sscr_198, retro_sscr_756, retro_sscr_807,
Ictidomys tridecemlineatus	ENSSTOG00000009841	2 retrocopies	retro_itri_1233, retro_itri_417,
Tarsius syrichta	ENSTSYG00000004848	16 retrocopies	retro_tsyr_1312, retro_tsyr_1340, retro_tsyr_1380, retro_tsyr_1399, retro_tsyr_1729, retro_tsyr_1914, retro_tsyr_1933, retro_tsyr_2161, retro_tsyr_357, retro_tsyr_455, retro_tsyr_469, retro_tsyr_581, retro_tsyr_606, retro_tsyr_642, retro_tsyr_703, retro_tsyr_856,
Tursiops truncatus	ENSTTRG00000006971	6 retrocopies	retro_ttru_1194, retro_ttru_171, retro_ttru_361, retro_ttru_498, retro_ttru_528, retro_ttru_915,
Vicugna pacos	ENSVPAG00000008894	2 retrocopies	retro_vpac_386, retro_vpac_584,