RetrogeneDB ID: retro_cjac_559

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:81224054..81224878(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000009124
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: EHD1
• Ensembl ID: ENSCJAG00000002660
• Aliases: None
• Description: None

Sequence

>retro_cjac_559
CCATAGCCTGAGCAATCAAGAATGCCTGTGTCATCATGCCCAGGCTCACTTATATTCCATTATCACCTCAGCAGAGGCTA
TGACTTTGCAGCTGTCCCGGAGTGGTTCGCCGAGCAGGTGGACGGAATCATCCTGCCCTTCGATGCCCATAAGCTGGAAA
TCTCTGATGAGTTCTCGGAAGTGATCAAGGCTCCGAAGAACCACAAGGACAAGATCCACGTGGTGCTGAACAAGGCAGAC
CAGATCCAGATGCAGCCGCTGATGCGGGTGTACGGGGCCCTCATGTGGTCCCTGGGCAGGATCATCAACACCCCCGAGGT
GGTCAGGGCCTACATCGGCTCCTTCTGGTCCTACCCACTCCTCATCCCCGACAACCGCGAGCTCTTTGAGGCTGAGGAGC
AGGACCTCTTCAAGGACATCCAGTCTCTGCCCCGAAATGCTGCCCTCAGGAAGCTCAATGACCTGATCAAGCGGGTGCGG
CTGGCCAAGGTTCACGCCTACATCATCAGCTCCCTCAAGGAGATGCCCAATGTCTTTGGGAAAGAGAGCAAAAAGAAAGA
GCTGGTGAACAACCTGGGAGAGATTACCAGAAGATCGAGCACGAGCACCAGATCTCCCCCGGTGACTTCCCGAGCCTCCG
CAAGATGCAGGAACTCCTGCAGACCCAGGACTTCAGCAAGTTCCAGGCCCTGAAGCCCGAGCTTCTGGATATGGTGGACA
ACATGCTGGCCAATGACATCGCACAGCTGATGGTGATGGTGCGGCAGGAGGAGTCCCTGATGCCTTCCCAGGTGGTCAAA
GGCAGCGCCTTTCACGGCACCATG

Alignment

ORF - retro_cjac_559 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.81 %
• Parental protein coverage: 54.31 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PNPVLDSISIIDTPGILSGEKQRISRGYDFAAVLEWFAERVDRIILLFDAHKLDISDEFSEVIKALKNHE
          P.P..........PG.L.......SRGYDFAAV.EWFAE.VD.IIL.FDAHKL.ISDEFSEVIKA.KNH.
Retrocopy P*PEQSRMPVSSCPGSLIFH-YHLSRGYDFAAVPEWFAEQVDGIILPFDAHKLEISDEFSEVIKAPKNHK

Parental  DKIRVVLNKADQIETQQLMRVYGALMWSLGKIINTPEVVRVYIGSFWSHPLLIPDNRKLFEAEEQDLFKD
          DKI.VVLNKADQI..Q.LMRVYGALMWSLG.IINTPEVVR.YIGSFWS.PLLIPDNR.LFEAEEQDLFKD
Retrocopy DKIHVVLNKADQIQMQPLMRVYGALMWSLGRIINTPEVVRAYIGSFWSYPLLIPDNRELFEAEEQDLFKD

Parental  IQSLPRNAALRKLNDLIKRARLAKVHAYIISSLKKEMPNVFGKESKKKELVNNLGEI-YQKIEREHQISP
          IQSLPRNAALRKLNDLIKR.RLAKVHAYIISSL.KEMPNVFGKESKKKELVNNLGEI.YQKIE.EHQISP
Retrocopy IQSLPRNAALRKLNDLIKRVRLAKVHAYIISSL-KEMPNVFGKESKKKELVNNLGEI<YQKIEHEHQISP

Parental  GDFPSLRKMQELLQTQDFNKFQALKPKLLDTVDDMLANDIARLMVMVRQEESLMPSQVVKGGAFDGTM
          GDFPSLRKMQELLQTQDF.KFQALKP.LLD.VD.MLANDIA.LMVMVRQEESLMPSQVVKG.AF.GTM
Retrocopy GDFPSLRKMQELLQTQDFSKFQALKPELLDMVDNMLANDIAQLMVMVRQEESLMPSQVVKGSAFHGTM

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
SRP051959_colon	0.00 RPM	26.49 RPM
SRP051959_heart	0.00 RPM	16.21 RPM
SRP051959_kidney	0.00 RPM	25.80 RPM
SRP051959_liver	0.00 RPM	8.53 RPM
SRP051959_lung	0.00 RPM	22.04 RPM
SRP051959_lymph_node	0.00 RPM	29.02 RPM
SRP051959_skeletal_muscle	0.00 RPM	20.94 RPM
SRP051959_spleen	0.00 RPM	19.87 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_559 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_559 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_559 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014128	1 retrocopy	retro_cfam_1713,
Callithrix jacchus	ENSCJAG00000002660	1 retrocopy	retro_cjac_559 ,
Callithrix jacchus	ENSCJAG00000007772	1 retrocopy	retro_cjac_3080,
Callithrix jacchus	ENSCJAG00000013985	1 retrocopy	retro_cjac_1122,
Sarcophilus harrisii	ENSSHAG00000005706	1 retrocopy	retro_shar_423,