RetrogeneDB ID: retro_cfam_339

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 10:1048123..1048509(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL27
• Ensembl ID: ENSCAFG00000014630
• Aliases: None
• Description: Canis lupus familiaris ribosomal protein L27 (RPL27), mRNA. [Source:RefSeq mRNA;Acc:NM_001003102]

Sequence

>retro_cfam_339
ATGGGCGAGTTCATGAAAGCCGGGAAGGCGGTGCTGGTCCTGGCTGGATGCCACTCTGGATGCAAACTGGTCATTGTGAA
GAACATTGGTGAGGGCATCCCAGACTGTCCCTATAGCCACACTCTGGTGTCTGGAATTGACCACTATGCCCACACAAAGT
GACAGCTGCCATGGGCAAGAAGGAAATCGCCAAGAGGTCAAAGATAAAATCTTTGGTGAAAGTTCACAACTACAATCACC
TCATGCCTATGAAGTACTCTGTGAATAGCCCCTTGGACAAAACTGACCTCAAACAGGATGTCTTCTGAGACCCTGCCCCT
AAATACAAGGCCTGAAGAAAGGCCAAGATCAAGTTCAAGGAGAGGTACAAGACTGGCAAGAACAAA

Alignment

ORF - retro_cfam_339 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.92 %
• Parental protein coverage: 94.12 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MGKFMKPGKVVLVLAGRYSGRKAVIVKNIDDGTSDRPYSHALVAGIDRY-PRKVTAAMGK-KKIAKRSKI
          MG.FMK.GK.VLVLAG..SG.K.VIVKNI..G..D.PYSH.LV.GID.Y.P.......G..K.IAKRSKI
Retrocopy MGEFMKAGKAVLVLAGCHSGCKLVIVKNIGEGIPDCPYSHTLVSGIDHY>PTQSDSCHGQ>KEIAKRSKI

Parental  KSFVKVYNYNHLMPTRYSVDIPLDKTVVNKDVFRDPALKRKARREAKVKFEERYKTGKNK
          KS.VKV.NYNHLMP..YSV..PLDKT....DVF.DPA.K.KA.R.AK.KF.ERYKTGKNK
Retrocopy KSLVKVHNYNHLMPMKYSVNSPLDKTDLKQDVF*DPAPKYKA*RKAKIKFKERYKTGKNK

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
SRP012049_cerebellum	0.00 RPM	185.72 RPM
SRP017611_brain	0.00 RPM	68.91 RPM
SRP017611_kidney	0.13 RPM	429.44 RPM
SRP017611_liver	0.00 RPM	94.34 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_339 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_339 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_339 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 32 parental genes, and 183 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000200	3 retrocopies	retro_amel_122, retro_amel_37, retro_amel_674,
Bos taurus	ENSBTAG00000017441	6 retrocopies	retro_btau_1113, retro_btau_129, retro_btau_1565, retro_btau_1855, retro_btau_338, retro_btau_394,
Canis familiaris	ENSCAFG00000014630	6 retrocopies	retro_cfam_1193, retro_cfam_2109, retro_cfam_339 , retro_cfam_364, retro_cfam_947, retro_cfam_959,
Callithrix jacchus	ENSCJAG00000013067	9 retrocopies	retro_cjac_1345, retro_cjac_1350, retro_cjac_1543, retro_cjac_1630, retro_cjac_2210, retro_cjac_275, retro_cjac_2828, retro_cjac_369, retro_cjac_776,
Cavia porcellus	ENSCPOG00000027359	3 retrocopies	retro_cpor_1178, retro_cpor_677, retro_cpor_715,
Dipodomys ordii	ENSDORG00000010907	6 retrocopies	retro_dord_154, retro_dord_335, retro_dord_477, retro_dord_527, retro_dord_601, retro_dord_784,
Equus caballus	ENSECAG00000007500	1 retrocopy	retro_ecab_132,
Echinops telfairi	ENSETEG00000002811	23 retrocopies	retro_etel_1230, retro_etel_1250, retro_etel_1302, retro_etel_1312, retro_etel_1453, retro_etel_1496, retro_etel_160, retro_etel_177, retro_etel_2055, retro_etel_2170, retro_etel_278, retro_etel_306, retro_etel_349, retro_etel_415, retro_etel_461, retro_etel_467, retro_etel_548, retro_etel_555, retro_etel_751, retro_etel_753, retro_etel_775, retro_etel_805, retro_etel_971,
Felis catus	ENSFCAG00000013142	6 retrocopies	retro_fcat_1026, retro_fcat_1184, retro_fcat_1824, retro_fcat_228, retro_fcat_698, retro_fcat_78,
Homo sapiens	ENSG00000131469	6 retrocopies	retro_hsap_1161, retro_hsap_1312, retro_hsap_2112, retro_hsap_2204, retro_hsap_238, retro_hsap_3787,
Gorilla gorilla	ENSGGOG00000026039	6 retrocopies	retro_ggor_1741, retro_ggor_1852, retro_ggor_2546, retro_ggor_2630, retro_ggor_298, retro_ggor_907,
Loxodonta africana	ENSLAFG00000014220	3 retrocopies	retro_lafr_443, retro_lafr_739, retro_lafr_965,
Microcebus murinus	ENSMICG00000014214	5 retrocopies	retro_mmur_1340, retro_mmur_1498, retro_mmur_1542, retro_mmur_673, retro_mmur_695,
Myotis lucifugus	ENSMLUG00000004119	1 retrocopy	retro_mluc_359,
Macaca mulatta	ENSMMUG00000008090	7 retrocopies	retro_mmul_1646, retro_mmul_1997, retro_mmul_418, retro_mmul_478, retro_mmul_52, retro_mmul_680, retro_mmul_925,
Monodelphis domestica	ENSMODG00000015128	1 retrocopy	retro_mdom_1141,
Mustela putorius furo	ENSMPUG00000009913	11 retrocopies	retro_mputfur_1041, retro_mputfur_1108, retro_mputfur_1182, retro_mputfur_1307, retro_mputfur_1530, retro_mputfur_303, retro_mputfur_413, retro_mputfur_595, retro_mputfur_675, retro_mputfur_735, retro_mputfur_980,
Mus musculus	ENSMUSG00000063316	2 retrocopies	retro_mmus_223, retro_mmus_277,
Nomascus leucogenys	ENSNLEG00000011901	2 retrocopies	retro_nleu_334, retro_nleu_45,
Oryctolagus cuniculus	ENSOCUG00000003872	1 retrocopy	retro_ocun_263,
Otolemur garnettii	ENSOGAG00000003940	14 retrocopies	retro_ogar_1091, retro_ogar_1297, retro_ogar_1478, retro_ogar_1692, retro_ogar_1887, retro_ogar_2189, retro_ogar_2354, retro_ogar_2625, retro_ogar_2687, retro_ogar_2915, retro_ogar_3207, retro_ogar_3294, retro_ogar_3381, retro_ogar_618,
Procavia capensis	ENSPCAG00000013249	4 retrocopies	retro_pcap_123, retro_pcap_146, retro_pcap_203, retro_pcap_227,
Pan troglodytes	ENSPTRG00000009232	6 retrocopies	retro_ptro_127, retro_ptro_1673, retro_ptro_208, retro_ptro_2569, retro_ptro_794, retro_ptro_900,
Pteropus vampyrus	ENSPVAG00000008817	4 retrocopies	retro_pvam_1084, retro_pvam_1231, retro_pvam_25, retro_pvam_509,
Rattus norvegicus	ENSRNOG00000020674	8 retrocopies	retro_rnor_1150, retro_rnor_125, retro_rnor_1257, retro_rnor_1968, retro_rnor_2594, retro_rnor_2989, retro_rnor_386, retro_rnor_414,
Sorex araneus	ENSSARG00000011131	10 retrocopies	retro_sara_254, retro_sara_292, retro_sara_493, retro_sara_498, retro_sara_547, retro_sara_611, retro_sara_62, retro_sara_672, retro_sara_685, retro_sara_696,
Sarcophilus harrisii	ENSSHAG00000012042	4 retrocopies	retro_shar_10, retro_shar_253, retro_shar_730, retro_shar_741,
Sus scrofa	ENSSSCG00000025507	5 retrocopies	retro_sscr_109, retro_sscr_1154, retro_sscr_576, retro_sscr_683, retro_sscr_943,
Ictidomys tridecemlineatus	ENSSTOG00000020555	5 retrocopies	retro_itri_1295, retro_itri_1812, retro_itri_283, retro_itri_836, retro_itri_926,
Tarsius syrichta	ENSTSYG00000003167	12 retrocopies	retro_tsyr_1032, retro_tsyr_1154, retro_tsyr_1711, retro_tsyr_2036, retro_tsyr_381, retro_tsyr_476, retro_tsyr_602, retro_tsyr_787, retro_tsyr_816, retro_tsyr_822, retro_tsyr_95, retro_tsyr_989,
Tursiops truncatus	ENSTTRG00000011739	2 retrocopies	retro_ttru_1049, retro_ttru_1535,
Vicugna pacos	ENSVPAG00000002574	1 retrocopy	retro_vpac_324,