RetrogeneDB ID: retro_cfam_906

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 2:62299361..62300239(+)
• Located in intron of: ENSCAFG00000009654

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL5
• Ensembl ID: ENSCAFG00000020150
• Aliases: None
• Description: ribosomal protein L5 [Source:HGNC Symbol;Acc:10360]

Sequence

>retro_cfam_906
TTTGTTAAAGTTGTCAAAAATAAGGCTTGCATCAAGAGATACCAAGTGAAATTTAGGTGAAGACAAGAAGGTAACACTGA
TTACTATGCTCAAAAATGGTTGGTAATTTAGGATAAAAATAAGTACAACACATCCAAATACAGGATGATAGTTCACATAA
TCAACAGAGATATCATTTGTCAGATTACTCATGCCTGTACAGAAGAAGACATGATAGTCTGTGCAGCTCATGCTCATGAA
CTCCCAAAGTATGGTGTGAAGGCTGGTCTGACAAATTATGCTGACAAATTATTGTACAGACCTGCTGCTGGCCCACAGGC
TTCTCAACAGGTTGGACAGGGACAAGATCTATGAAGGCCAAGTGGAAGTGACAGGAGATGAATACAATGTGGAAAGCATT
GATGGTCAACCTGGTACCTTCACCTGCTATGTGGATGCAGGGCTGGCCAGAACTACTACTGGAAATAAAGTTTTGGGGGC
CCTCAAGGGAGCTGTGGATGGAGGCTTGTCTGTTGCTCAGAGTACCAAACAATTTCTTGGTTATGATGTGGAAAGTAAGG
AATTCAATGCAGAAGTACATCTGAAGCACGTCATGGGTCAGATTATTGCAGATCTATTGTGTTACCTAATGGAAGAAGAT
GAAGATACCTACAAGGAACAACTCTGTCAATACATGAAGAACAAAGCATCTTCAGATATGGAGGAGATATAAAGAAAGCT
CATGCTGCCACATGAGAGAACCCAATCTATGAGAAGAAGCCTAAGAAAGAAGTTAGAAAGAAGAGGGGGAACCACCCAAG
ATGTCTCTTGCCCAGAAGAAATATTAGGTAGCTCAGAAGACAAGCTTCCTTAGAGCTCAGGAGCAGGCTGCTGGAAGC

Alignment

ORF - retro_cfam_906 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.51 %
• Parental protein coverage: 99.33 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  FVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDIICQIAYARIEGD
          FVKVVKNKA..KRYQVKFR.R.EG.TDYYA.K.LVI.DKNKYNT.KYRMIV...NRDIICQI..A..E.D
Retrocopy FVKVVKNKACIKRYQVKFR*RQEGNTDYYAQKWLVI*DKNKYNTSKYRMIVHIINRDIICQITHACTEED

Parental  MIVCAAYAHELPKYGVKVGLTNYA-AAYCTGLLLARRLLNRFGMDKIYEGQVEVTGDEYNVESIDGQPGA
          MIVCAA.AHELPKYGVK.GLTNYA...YCT.LLLA.RLLNR...DKIYEGQVEVTGDEYNVESIDGQPG.
Retrocopy MIVCAAHAHELPKYGVKAGLTNYA>TNYCTDLLLAHRLLNRLDRDKIYEGQVEVTGDEYNVESIDGQPGT

Parental  FTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRFPGYDSESKEFNAEVHRKHIMGQNVADYMRYL
          FTCY.DAGLARTTTGNKV.GALKGAVDGGLS...STK.F.GYD.ESKEFNAEVH.KH.MGQ..AD...YL
Retrocopy FTCYVDAGLARTTTGNKVLGALKGAVDGGLSVAQSTKQFLGYDVESKEFNAEVHLKHVMGQIIADLLCYL

Parental  MEEDEDAYKKQFSQYIKNNVTPDMMEEMYKK-AHAAIRENPVYEKKPKKEVKKKRWNR-PKMSLAQKKDR
          MEEDED.YK.Q..QY.KN....D.MEE...K.AHAA..ENP.YEKKPKKEV.KKR.N..PKMSLAQKK..
Retrocopy MEEDEDTYKEQLCQYMKNKASSD-MEEI*RK<AHAAT*ENPIYEKKPKKEVRKKRGNH<PKMSLAQKKY*

Parental  VAQKKASFLRAQERAAES
          VAQ.K.SFLRAQE.AA.S
Retrocopy VAQ-KTSFLRAQEQAAGS

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	0.13 RPM	296.85 RPM
SRP017611_brain	0.08 RPM	121.23 RPM
SRP017611_kidney	0.00 RPM	549.17 RPM
SRP017611_liver	0.00 RPM	265.18 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_906 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_906 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_906 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 67 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000020150	4 retrocopies	retro_cfam_1505, retro_cfam_1696, retro_cfam_905, retro_cfam_906 ,
Felis catus	ENSFCAG00000024680	5 retrocopies	retro_fcat_281, retro_fcat_304, retro_fcat_453, retro_fcat_458, retro_fcat_463,
Loxodonta africana	ENSLAFG00000011916	6 retrocopies	retro_lafr_1025, retro_lafr_1098, retro_lafr_302, retro_lafr_988, retro_lafr_989, retro_lafr_992,
Macropus eugenii	ENSMEUG00000006361	3 retrocopies	retro_meug_1168, retro_meug_1537, retro_meug_2146,
Myotis lucifugus	ENSMLUG00000008956	1 retrocopy	retro_mluc_925,
Monodelphis domestica	ENSMODG00000011635	1 retrocopy	retro_mdom_748,
Nomascus leucogenys	ENSNLEG00000010500	2 retrocopies	retro_nleu_2102, retro_nleu_39,
Ornithorhynchus anatinus	ENSOANG00000004669	1 retrocopy	retro_oana_97,
Procavia capensis	ENSPCAG00000011865	2 retrocopies	retro_pcap_159, retro_pcap_201,
Petromyzon marinus	ENSPMAG00000002040	1 retrocopy	retro_pmar_23,
Pongo abelii	ENSPPYG00000001152	32 retrocopies	retro_pabe_1053, retro_pabe_1219, retro_pabe_1274, retro_pabe_1307, retro_pabe_1331, retro_pabe_1501, retro_pabe_1918, retro_pabe_1931, retro_pabe_2019, retro_pabe_2123, retro_pabe_2238, retro_pabe_2457, retro_pabe_246, retro_pabe_247, retro_pabe_2640, retro_pabe_2641, retro_pabe_2658, retro_pabe_2813, retro_pabe_2841, retro_pabe_2909, retro_pabe_3247, retro_pabe_3320, retro_pabe_3360, retro_pabe_3534, retro_pabe_446, retro_pabe_447, retro_pabe_480, retro_pabe_51, retro_pabe_562, retro_pabe_572, retro_pabe_637, retro_pabe_740,
Sarcophilus harrisii	ENSSHAG00000006417	1 retrocopy	retro_shar_202,
Tarsius syrichta	ENSTSYG00000014038	8 retrocopies	retro_tsyr_1462, retro_tsyr_1548, retro_tsyr_206, retro_tsyr_248, retro_tsyr_670, retro_tsyr_737, retro_tsyr_786, retro_tsyr_952,