RetrogeneDB ID: retro_cfam_1009

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 21:18135331..18135698(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL28
• Ensembl ID: ENSCAFG00000002585
• Aliases: None
• Description: ribosomal protein L28 [Source:HGNC Symbol;Acc:10330]

Sequence

>retro_cfam_1009
TGGATGATAATGCAGAACAGCTCCAACTTCCTGGTCAAGAAGAACAAACAGACATACAGCACAGAATCACATAATCTGAA
GCTTGCAACTCCTTCTGCCACGAAAAGCTGATTCACTGCAAGACTATGGGCATGGAGCTGCCAGCCTATGGCCAATGTGT
AGTGGTAGTCATTAATTGGAAATCTGACCAGCAAACCCCACCACTTCCTATGTGTGGACCACTATTAGTAAGAATGCCCA
GGCCATCCTCAGCAGTATCAGGCACATGATCTGCAAGAACAAGTACAGCTCAGATCTGCACATAGCTGGCATTTGCAGAG
CCAGCACCATCCTGCCTAGCCAGAAATTTGTGATGGTGAGGAGGAAG

Alignment

ORF - retro_cfam_1009 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.4 %
• Parental protein coverage: 89.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  WMVVRNCSSFLIKRNKQTYSTEPNNLK-ARNSFRYNGLIHRKTVGVEPAADGKGVVVVLKRRSGQR-KPA
          WM...N.S.FL.K.NKQTYSTE..NLK.A.NSF....LIH.KT.G.E..A.G..VVVV....S.Q...P.
Retrocopy WMIMQNSSNFLVKKNKQTYSTESHNLK<ACNSFCHEKLIHCKTMGMELPAYGQCVVVVINWKSDQQ<NPT

Parental  TSYVRTTINKNARATLSSIRHMIRKNKYRPDLRMAAIRRASAILRSQKPVMVKRK
          TSYV.TTI.KNA.A.LSSIRHMI.KNKY..DL..A.I.RAS.IL.SQK.VMV.RK
Retrocopy TSYVWTTISKNAQAILSSIRHMICKNKYSSDLHIAGICRASTILPSQKFVMVRRK

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	183.03 RPM
SRP017611_brain	0.00 RPM	48.35 RPM
SRP017611_kidney	0.00 RPM	297.70 RPM
SRP017611_liver	0.00 RPM	121.02 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1009 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1009 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1009 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 69 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000015980	1 retrocopy	retro_acar_10,
Ailuropoda melanoleuca	ENSAMEG00000003764	15 retrocopies	retro_amel_1006, retro_amel_1099, retro_amel_1155, retro_amel_1369, retro_amel_1393, retro_amel_1465, retro_amel_1737, retro_amel_231, retro_amel_289, retro_amel_33, retro_amel_474, retro_amel_556, retro_amel_630, retro_amel_822, retro_amel_829,
Canis familiaris	ENSCAFG00000002585	8 retrocopies	retro_cfam_1009 , retro_cfam_1192, retro_cfam_2145, retro_cfam_350, retro_cfam_462, retro_cfam_533, retro_cfam_581, retro_cfam_879,
Callithrix jacchus	ENSCJAG00000000869	1 retrocopy	retro_cjac_218,
Cavia porcellus	ENSCPOG00000012833	2 retrocopies	retro_cpor_127, retro_cpor_214,
Felis catus	ENSFCAG00000005639	15 retrocopies	retro_fcat_1045, retro_fcat_1214, retro_fcat_1397, retro_fcat_1404, retro_fcat_1463, retro_fcat_1629, retro_fcat_1663, retro_fcat_171, retro_fcat_233, retro_fcat_484, retro_fcat_575, retro_fcat_786, retro_fcat_904, retro_fcat_910, retro_fcat_942,
Loxodonta africana	ENSLAFG00000022257	2 retrocopies	retro_lafr_325, retro_lafr_548,
Macropus eugenii	ENSMEUG00000015744	1 retrocopy	retro_meug_1497,
Myotis lucifugus	ENSMLUG00000023789	1 retrocopy	retro_mluc_325,
Macaca mulatta	ENSMMUG00000015901	1 retrocopy	retro_mmul_68,
Monodelphis domestica	ENSMODG00000000275	1 retrocopy	retro_mdom_1458,
Mus musculus	ENSMUSG00000030432	10 retrocopies	retro_mmus_162, retro_mmus_1679, retro_mmus_1911, retro_mmus_2511, retro_mmus_2526, retro_mmus_2606, retro_mmus_2629, retro_mmus_3149, retro_mmus_362, retro_mmus_738,
Ochotona princeps	ENSOPRG00000000463	1 retrocopy	retro_opri_686,
Petromyzon marinus	ENSPMAG00000008617	1 retrocopy	retro_pmar_10,
Pongo abelii	ENSPPYG00000010417	4 retrocopies	retro_pabe_1691, retro_pabe_1869, retro_pabe_2383, retro_pabe_2778,
Rattus norvegicus	ENSRNOG00000017127	5 retrocopies	retro_rnor_1588, retro_rnor_2117, retro_rnor_243, retro_rnor_610, retro_rnor_855,