RetrogeneDB ID: retro_cfam_2073

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:44701515..44702571(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF3H
• Ensembl ID: ENSCAFG00000000816
• Aliases: None
• Description: eukaryotic translation initiation factor 3, subunit H [Source:HGNC Symbol;Acc:3273]

Sequence

>retro_cfam_2073
ATGGCATCCCGCAAGGAAGGCACCGGCTCTGCTGCCCCTTCTTCCAGCTCCACCACCGGCCAGGTGGGGAAAGGCAAAGG
CAAAGGCGGGTCCAGAGATTCTGCCGTGAAACAAGGGCAGATAGATGGCTTGGTGGTATTAAAAATAATCGAACATTATC
AAGAAGAGGGACAAGCAACCGAAGTGGTTCAAGAAGTGCTTTTGGGCTTGGTTGTAGAAGATTGACTTGAAATTACCAAC
TGCTTCCCTTTCCCCCAGCACACAGAAGATGATGCTGATTTTGATGAAGTCCAGTATCAGGTGGAAATGATGTGCAGCCT
TTGCCATGTCAACATCAATCACCTCCACGTGGGCTGGTACCAGTCCACATACTATGGTTTGTTCGTCACCTGAGCACTCC
TGGATTCTCAGTTCAGTTACCAGCATGCCATTGAAGAATCTGTCGTTCTCATTTACAATCCCATAAAAGCTGCCCAAGGG
TCTCTCTCGCTGAAAGCATACAGACTGACTCCTAAACTAATGGAAGTTTGTGAAGAGAAGGATTTTTCTCCTGAAGCATT
GAAAAAGGGAAATATCACCTTTGAGCACACGTTTGAAGAAGTGCCGATTGGAATTAAAAATTCACATCTGATCAACGTCC
TATTGTGGGAGCTTGAGAAGAAGTCAGCTGTAGCAGATAAACATGAATTGCTCAGTCTTGCTAGCAGCAATCATTTGGGG
AAGAATCTACAGTTGCTGATGGACAGAGTGGATGAAATGAGCCAAGATATAGTTAAATATAACACATACATGAGGAACAC
GAGTAAACAACAGCAGCAGAAACGTCAGTATCAGCAGCCTCGCCGGCAGGAGAATATGCAGCACCAGAGTCAAAGAGAAG
CCCCACTGCCTGAGGAGGATCTGTCCAAACTTTTCAAACCACCCCAGCCTCCTGCCAGGATGGATTCTCTACTCATTGCA
GGCCAGATTAACACTTACTGCCAGAACATCAAGGAGTTCACTGCCCAAAACTTAGGCAAACTCTTCATGGCCCAGGCTCT
TCAGGAATACAACAAC

Alignment

ORF - retro_cfam_2073 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.76 %
• Parental protein coverage: 93.37 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASRKEGAGSAATSSSSTTGPAGKGKGKGGSGDSAVKQVQIDGLVVLKIIKHYQEEGQGTEVVQGVLLGL
          MASRKEG.GSAA.SSSSTTG..GKGKGKGGS.DSAVKQ.QIDGLVVLKII.HYQEEGQ.TEVVQ.VLLGL
Retrocopy MASRKEGTGSAAPSSSSTTGQVGKGKGKGGSRDSAVKQGQIDGLVVLKIIEHYQEEGQATEVVQEVLLGL

Parental  VVEDRLEITNCFPFPQHTEDDADFDEVQYQMEMMRSLRHVNIDHLHVGWYQSTYYGSFVTRALLDSQFSY
          VVED.LEITNCFPFPQHTEDDADFDEVQYQ.EMM.SL.HVNI.HLHVGWYQSTYYG.FVT.ALLDSQFSY
Retrocopy VVED*LEITNCFPFPQHTEDDADFDEVQYQVEMMCSLCHVNINHLHVGWYQSTYYGLFVT*ALLDSQFSY

Parental  QHAIEESVVLIYDPIKTAQGSLSLKAYRLTPKLMEVCKEKDFSPEALKKGNITFEHMFEEVPIVIKNSHL
          QHAIEESVVLIY.PIK.AQGSLSLKAYRLTPKLMEVC.EKDFSPEALKKGNITFEH.FEEVPI.IKNSHL
Retrocopy QHAIEESVVLIYNPIKAAQGSLSLKAYRLTPKLMEVCEEKDFSPEALKKGNITFEHTFEEVPIGIKNSHL

Parental  INVLMWELEKKSAVADKHELLSLASSNHLGKNLQLLMDRVDEMSQDIVKYNTYMRNTSKQQQQKHQYQQR
          INVL.WELEKKSAVADKHELLSLASSNHLGKNLQLLMDRVDEMSQDIVKYNTYMRNTSKQQQQK.QYQQ.
Retrocopy INVLLWELEKKSAVADKHELLSLASSNHLGKNLQLLMDRVDEMSQDIVKYNTYMRNTSKQQQQKRQYQQP

Parental  RQQENMQRQSRGEPPLPEEDLSKLFKPPQPPARMDSLLIAGQINTYCQNIKEFTAQNLGKLFMAQALQEY
          R.QENMQ.QS..E.PLPEEDLSKLFKPPQPPARMDSLLIAGQINTYCQNIKEFTAQNLGKLFMAQALQEY
Retrocopy RRQENMQHQSQREAPLPEEDLSKLFKPPQPPARMDSLLIAGQINTYCQNIKEFTAQNLGKLFMAQALQEY

Parental  NN
          NN
Retrocopy NN

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	0.25 RPM	95.80 RPM
SRP017611_brain	0.32 RPM	49.14 RPM
SRP017611_kidney	0.33 RPM	182.79 RPM
SRP017611_liver	0.36 RPM	49.02 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

1 EST(s) were mapped to retro_cfam_2073 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
DN378647	44701977	44702105	100	126	0	124

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2073 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2073 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000816	1 retrocopy	retro_cfam_2073 ,
Callithrix jacchus	ENSCJAG00000005910	1 retrocopy	retro_cjac_3023,
Echinops telfairi	ENSETEG00000000324	1 retrocopy	retro_etel_24,
Macropus eugenii	ENSMEUG00000015663	4 retrocopies	retro_meug_1223, retro_meug_1244, retro_meug_1790, retro_meug_376,
Monodelphis domestica	ENSMODG00000004154	1 retrocopy	retro_mdom_1243,
Mus musculus	ENSMUSG00000022312	1 retrocopy	retro_mmus_1668,
Oryctolagus cuniculus	ENSOCUG00000007534	1 retrocopy	retro_ocun_608,
Otolemur garnettii	ENSOGAG00000008905	1 retrocopy	retro_ogar_2043,
Sorex araneus	ENSSARG00000009067	1 retrocopy	retro_sara_69,
Sarcophilus harrisii	ENSSHAG00000014977	1 retrocopy	retro_shar_561,
Ictidomys tridecemlineatus	ENSSTOG00000001403	1 retrocopy	retro_itri_420,