RetrogeneDB ID: retro_cjac_4030

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL289951.1:398754..399765(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000023300
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ABCD4
• Ensembl ID: ENSCJAG00000020446
• Aliases: None
• Description: None

Sequence

>retro_cjac_4030
TGGCTGTACATCGGCATCAACACCTTTGACTATCTGGGCAGCATACTGAATCACACTGTCATCGCAATCCCCATTTTCAG
TTGGGTCTTTGGAGAACTGAGTCCTGCAGATCTTAGCATCCTGGTTAGCAAGAACGCCTTTGTGTGCATCTACCTCATCA
GCTGCTTCACTCAGCTCATTGACCTGTCCACAATGCTCTTGGATGTGGCTGACTACACGCACAGGATTGGGCAGCTTCGG
GAGACGCTGCTGGACATGTCCTTGAAGTCACAGGCCTGTGAGATCCTGGGCGAGAGCGGGTGGGCTTGGACAAGGCTCCC
GGATGGCCAGCAGCAGAGCCAGCAGACACGGCATTTCTCCTTGAGCGGGTCTCCATCTCTGCTCCCTCGTCTGACAAACC
CCTAATCAAGGATCTGAGCCTACAGATCTCTGAGGGATAGAGCCTGCTCATCACAGGCAATACGGGCACTGGCAAGACCT
CCTTGCCCCGGGCTCTGGGCGACCTCTGGACGAGCACACGGGACTCAGTGCAAATGCTGACAGACTTTGGGCACCATGGG
GTGCTATTCCTGCCAAAAAAGCTGTTCTTCACTGGCGGGACCCTTCGGGAGCAGGTGATATATCCCCTGAAGGAGATTTA
TCCTGACTCACGTTTTACTGATGATGAGAAGATCTTGAGGTTCTTGGAATTGGCAGGCCTGTCCAGCTTGGTGGCAAGGA
CAGAGGATCTGGACCAGCATGTGGATTGGAATTGGTATGATGTTCTGTCCCTGGGGGAGATGCAACGGCTCTCCTTTGCC
CGACTCTTCTACCTGCAGCCTGAAGTATGCAGTGCTTGATGAAGCCACCAGTGCCCTGATAGAGGAGATGGAGAGCAAGC
TCTATCGCATCAGCCAGCAGTTGGAGATGACGTTCATCAGTGTGGGGCATCGACAGAGCCTTAAGTTTCATTCCTTGGTT
CTGAAACTCTGTGGAGGAGGAATATGGGAACTGATGAGAATCAAACAGGAA

Alignment

ORF - retro_cjac_4030 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.68 %
• Parental protein coverage: 55.85 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  WLYIGINTFDYLGSILSYVVIAIPIFSGVYGDLSPAELSILVSKNAFVCIYLISCFTQLIDLCTTLSDVA
          WLYIGINTFDYLGSIL...VIAIPIFS.V.G.LSPA.LSILVSKNAFVCIYLISCFTQLIDL.T.L.DVA
Retrocopy WLYIGINTFDYLGSILNHTVIAIPIFSWVFGELSPADLSILVSKNAFVCIYLISCFTQLIDLSTMLLDVA

Parental  GYTHRIGQLRETLLDMSLKSQDCEILGESEW-GLDKTPGWPAAEPADMAFLLERVSISVPSSDKPLIKDL
          .YTHRIGQLRETLLDMSLKSQ.CEILGES.W.GLDK.PGWPAAEPAD.AFLLERVSIS.PSSDKPLIKDL
Retrocopy DYTHRIGQLRETLLDMSLKSQACEILGESGW<GLDKAPGWPAAEPADTAFLLERVSISAPSSDKPLIKDL

Parental  SLQISEGQSLLITGNTGTGKTSLLRVLGGLWTSTRGSVQMLTDFGPHGVLFLPQKPFFTDGTLREQQVIY
          SLQISEG.SLLITGNTGTGKTSL.R.LG.LWTSTR.SVQMLTDFG.HGVLFLP.K.FFT.GTLRE.QVIY
Retrocopy SLQISEG*SLLITGNTGTGKTSLPRALGDLWTSTRDSVQMLTDFGHHGVLFLPKKLFFTGGTLRE-QVIY

Parental  PLKEIYPDSGSTDDERILRFLELAGLSSLVARTEGLDQQVDWNWYDVLSPGEMQRLSFARLFYLQP-KYA
          PLKEIYPDS..TDDE.ILRFLELAGLSSLVARTE.LDQ.VDWNWYDVLS.GEMQRLSFARLFYLQP.KYA
Retrocopy PLKEIYPDSRFTDDEKILRFLELAGLSSLVARTEDLDQHVDWNWYDVLSLGEMQRLSFARLFYLQP>KYA

Parental  VLDEATSALTEEVESELYRIGQQLGMTFISVGHRQSLEKFHSLVLKLCGGGRWELMRIKEE
          VLDEATSAL.EE.ES.LYRI.QQL.MTFISVGHRQSL.KFHSLVLKLCGGG.WELMRIK.E
Retrocopy VLDEATSALIEEMESKLYRISQQLEMTFISVGHRQSL-KFHSLVLKLCGGGIWELMRIKQE

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	17.53 RPM
SRP051959_heart	0.11 RPM	8.51 RPM
SRP051959_kidney	0.00 RPM	13.60 RPM
SRP051959_liver	0.00 RPM	14.40 RPM
SRP051959_lung	0.02 RPM	15.21 RPM
SRP051959_lymph_node	0.00 RPM	23.70 RPM
SRP051959_skeletal_muscle	0.00 RPM	5.18 RPM
SRP051959_spleen	0.00 RPM	17.86 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4030 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4030 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4030 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020446	1 retrocopy	retro_cjac_4030 ,