RetrogeneDB ID: retro_cfam_1311

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 29:27622259..27622715(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000032349
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPS18
• Ensembl ID: ENSCAFG00000000950
• Aliases: None
• Description: Canis lupus familiaris ribosomal protein S18 (RPS18), mRNA. [Source:RefSeq mRNA;Acc:NM_001048082]

Sequence

>retro_cfam_1311
ATGTCTCTAGTGATCCCTGAGAAGTTCTAGCACATTTTGTGAGTAATCAACACCAATATGGATGGGCGGCAGAAAATGGG
CTTTGCCATCACAGCAATTAAGGGCGTGGGGCGAAGATATGCTCATGTGGTGTTGAGAAAAGCAGACATCTAGCTCACCA
AGAGAGCCAGAGAGCTCACTGAGGATGAAATGGAACGTGTGATCACCATTATGCAGAGTCCATGCCAGTATAAGATCCCA
GGCTGGTTTTTGAACAGACAAAAGGATGTGAAGGATGGAAAGTACAGCCAGGTCCTGGCCAATGGTCTGGACAACAAACT
TCGTGAAGACCTGGAGAGACTGAAGAAGATTCGAGCCCACAGGGGGCTGCACCACTTCTGGGGACTTCATGTCCAAGGCC
AGCACACCAAGACCACAGAGTGCTGTGTTCGCACCATGGGTGTATCCAAGAAGAAA

Alignment

ORF - retro_cfam_1311 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.18 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSLVIPEKFQHILRVLNTNIDGRRKIAFAITAIKGVGRRYAHVVLRKADIDLTKRAGELTEDEVERVITI
          MSLVIPEKF.HIL.V.NTN.DGR.K..FAITAIKGVGRRYAHVVLRKADI.LTKRA.ELTEDE.ERVITI
Retrocopy MSLVIPEKF*HIL*VINTNMDGRQKMGFAITAIKGVGRRYAHVVLRKADI*LTKRARELTEDEMERVITI

Parental  MQNPRQYKIPDWFLNRQKDVKDGKYSQVLANGLDNKLREDLERLKKIRAHRGLRHFWGLRVRGQHTKTTG
          MQ.P.QYKIP.WFLNRQKDVKDGKYSQVLANGLDNKLREDLERLKKIRAHRGL.HFWGL.V.GQHTKTT.
Retrocopy MQSPCQYKIPGWFLNRQKDVKDGKYSQVLANGLDNKLREDLERLKKIRAHRGLHHFWGLHVQGQHTKTTE

Parental  RRGRTVGVSKKK
          ...RT.GVSKKK
Retrocopy CCVRTMGVSKKK

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	228.26 RPM
SRP017611_brain	0.16 RPM	90.43 RPM
SRP017611_kidney	0.00 RPM	675.30 RPM
SRP017611_liver	0.07 RPM	191.73 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1311 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1311 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1311 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 57 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000950	7 retrocopies	retro_cfam_1311 , retro_cfam_1607, retro_cfam_2132, retro_cfam_414, retro_cfam_522, retro_cfam_789, retro_cfam_856,
Dipodomys ordii	ENSDORG00000013825	6 retrocopies	retro_dord_185, retro_dord_326, retro_dord_426, retro_dord_481, retro_dord_50, retro_dord_772,
Gorilla gorilla	ENSGGOG00000006571	5 retrocopies	retro_ggor_1496, retro_ggor_2310, retro_ggor_344, retro_ggor_77, retro_ggor_93,
Loxodonta africana	ENSLAFG00000032173	1 retrocopy	retro_lafr_1171,
Macaca mulatta	ENSMMUG00000003867	1 retrocopy	retro_mmul_2198,
Mus musculus	ENSMUSG00000008668	2 retrocopies	retro_mmus_57, retro_mmus_66,
Nomascus leucogenys	ENSNLEG00000006840	10 retrocopies	retro_nleu_1074, retro_nleu_1161, retro_nleu_1176, retro_nleu_1466, retro_nleu_219, retro_nleu_2572, retro_nleu_2616, retro_nleu_525, retro_nleu_60, retro_nleu_737,
Oryctolagus cuniculus	ENSOCUG00000010546	1 retrocopy	retro_ocun_31,
Procavia capensis	ENSPCAG00000005854	2 retrocopies	retro_pcap_235, retro_pcap_319,
Pongo abelii	ENSPPYG00000025953	14 retrocopies	retro_pabe_1138, retro_pabe_128, retro_pabe_1481, retro_pabe_1482, retro_pabe_1813, retro_pabe_1881, retro_pabe_2303, retro_pabe_2407, retro_pabe_2663, retro_pabe_2833, retro_pabe_2967, retro_pabe_3013, retro_pabe_3070, retro_pabe_368,
Pan troglodytes	ENSPTRG00000018039	1 retrocopy	retro_ptro_121,
Rattus norvegicus	ENSRNOG00000028505	4 retrocopies	retro_rnor_102, retro_rnor_234, retro_rnor_29, retro_rnor_70,
Sarcophilus harrisii	ENSSHAG00000006857	2 retrocopies	retro_shar_265, retro_shar_563,
Sarcophilus harrisii	ENSSHAG00000008658	1 retrocopy	retro_shar_618,