RetrogeneDB ID: retro_cjac_3424

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01179083.1:12465..13715(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000037625
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RCC1
• Ensembl ID: ENSCJAG00000009686
• Aliases: None
• Description: regulator of chromosome condensation [Source:RefSeq peptide;Acc:NP_001192137]

Sequence

>retro_cjac_3424
ATGCCACCCAAGCACATAGCTAAAAGAAGGTCACCCCCAGAAGATGCCATCCCCCAAAACAAGAAGGTGAAGGGCTCACA
CAGGTCCCACAGCACAGAACCAGGCTTAGTGCTGACACTGGGCCAAAGTGACGTGGGCCAGCTGGGGCTGAGTGAGAATG
TGATGGAGAGGAAGAAGCCGTCCCTGGTATCCATTCCAGAGGATGTTGTGCAGGCTGAGGCTGGGGGCATGCATACCAAG
TGTCTAAGCAAAAGTGGCCAGGTCTACTCCTTTGGCTGCAATGATGAGGGTGCCCTGGGAAAAGACATGTAAGTGGAGGG
CTCCGAAATGCTCCCTGGGAAAGTGGAGCTGCAAGAGAAGGTGTCAGCAGGAGATAGTCACACAGCAGCCCTCACCCAGG
ATGGTTGTGTCTTCCTCTGGGGCTCCTTCCAGGATAACAACGGTGTGATCAGACTGTTGGAGCCCATGAAGAAGAGAATG
GTGCCCGTACCCATCCAGCTAGATGTGCCTGTGGTGAAAGTGTCCTCAGGAAATGACCACTTGGTGATGCTGACAGCTGT
TGGTGACCTCTACACCTTGGACTGTGGGGAACAGGGCCAGCTAGGCTGTGTGCCTGAGTTATTTGCCAACTATGGTGGCC
GGCAAGGCCTTGAACGACTCCTGGTCTTCAAGTATGTGATGCTGAAATCCAGGGGAATCTGGGGCCATGTAAGATTCCAG
GATGCCTTCTGTGGTGCCTATTTCACCTTTGCCATCTCTCAAGAGGGCTACGTGTACAACTTTGGCCTCTCCAACTACCA
TCAGCTTGGAACTCCAGGCACAGAATTTTGTTTCATACCCCAGAACCTAATATCCTTCAAGAATTCCACCAAGTCCTGGG
TGGGTTTCTCTGGTGGCCAGCACCATATAGTCTGCAGGGATTCAGAAGGAAAAGCATACAGCATGGGCAGGGCTGAATAT
GGGCAGTGGGGCCTCGGGGAGGGTGCTGAGAAGAGCATACCCACCCTCATCGCCAGGCTGCCTGCTGTCTCCTCAGTGGC
TTGTGGGGCCTCTGTGGGGTATGCTGTGACCAAGGATGGTCATGTTTTGCCTGGGGCATGGGCATCAACTACCAGCTGGG
CACAGGGCAGGATGAAGATGCCTGGAGCCCTGTGGAGATGACAGGCAAAAAGCTGGAGAACCGTGTGGTCTTACCTGTGT
CCAGCAGGGGCCAGCATACAGTCTTATTAGTCAAGGATGGGTAACAGAGC

Alignment

ORF - retro_cjac_3424 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.44 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPPKRIAKRKSPPEDAIPKNKKVKVSHRSHSTEPGLVLTLGQGDVGQLGLGENVMERKKPALVSIPEDVV
          MPPK.IAKR.SPPEDAIP.NKKVK.SHRSHSTEPGLVLTLGQ.DVGQLGL.ENVMERKKP.LVSIPEDVV
Retrocopy MPPKHIAKRRSPPEDAIPQNKKVKGSHRSHSTEPGLVLTLGQSDVGQLGLSENVMERKKPSLVSIPEDVV

Parental  QAEAGGMHTVCLSKSGQVYSFGCNDEGALGRDTSVEGSEMVPGKVELQEKVVQVSAGDSHTAALTEDGRV
          QAEAGGMHT.CLSKSGQVYSFGCNDEGALG.D..VEGSEM.PGKVELQEK...VSAGDSHTAALT.DG.V
Retrocopy QAEAGGMHTKCLSKSGQVYSFGCNDEGALGKDM*VEGSEMLPGKVELQEK---VSAGDSHTAALTQDGCV

Parental  FLWGSFRDNNGVIGLLEPMKKSMVPVQVQLDVTVVKVASGNDHLVMLTADGDLYTLGCGEQGQLGRVPEL
          FLWGSF.DNNGVI.LLEPMKK.MVPV..QLDV.VVKV.SGNDHLVMLTA.GDLYTL.CGEQGQLG.VPEL
Retrocopy FLWGSFQDNNGVIRLLEPMKKRMVPVPIQLDVPVVKVSSGNDHLVMLTAVGDLYTLDCGEQGQLGCVPEL

Parental  FANRGGRQGLERLLVPKCVMLKSRGSRGHVRFQDAFCGAYFTFAISREGHVYGFGLSNYHQLGTPGTESC
          FAN.GGRQGLERLLV.K.VMLKSRG..GHVRFQDAFCGAYFTFAIS.EG.VY.FGLSNYHQLGTPGTE.C
Retrocopy FANYGGRQGLERLLVFKYVMLKSRGIWGHVRFQDAFCGAYFTFAISQEGYVYNFGLSNYHQLGTPGTEFC

Parental  FIPQNLTSFKNSTKSWVRFSGGQHHTVCMDSEGKAYSLGRAEYGRLGLGEGAEEKSIPTLISRLPAVSSV
          FIPQNL.SFKNSTKSWV.FSGGQHH.VC.DSEGKAYS.GRAEYG..GLGEGA.EKSIPTLI.RLPAVSSV
Retrocopy FIPQNLISFKNSTKSWVGFSGGQHHIVCRDSEGKAYSMGRAEYGQWGLGEGA-EKSIPTLIARLPAVSSV

Parental  ACGASVGYAVTKDGRV-FAWGMGTNYQLGTGQDEDAWSPVEMTGKQLENRVVLSVSSGGQHTVLLVKDKE
          ACGASVGYAVTKDG.V.FAWGMG.NYQLGTGQDEDAWSPVEMTGK.LENRVVL.VSS.GQHTVLLVKD..
Retrocopy ACGASVGYAVTKDGHV<FAWGMGINYQLGTGQDEDAWSPVEMTGKKLENRVVLPVSSRGQHTVLLVKDG*

Parental  QS
          QS
Retrocopy QS

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	7.97 RPM
SRP051959_heart	0.00 RPM	2.26 RPM
SRP051959_kidney	0.00 RPM	4.64 RPM
SRP051959_liver	0.00 RPM	6.39 RPM
SRP051959_lung	0.02 RPM	5.27 RPM
SRP051959_lymph_node	0.00 RPM	9.00 RPM
SRP051959_skeletal_muscle	0.00 RPM	2.25 RPM
SRP051959_spleen	0.00 RPM	5.92 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3424 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3424 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3424 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009686	3 retrocopies	retro_cjac_2440, retro_cjac_3424 , retro_cjac_3856,
Erinaceus europaeus	ENSEEUG00000004565	1 retrocopy	retro_eeur_418,
Myotis lucifugus	ENSMLUG00000017075	1 retrocopy	retro_mluc_2278,
Rattus norvegicus	ENSRNOG00000050106	1 retrocopy	retro_rnor_2886,