RetrogeneDB ID: retro_cjac_2542

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:84369032..84370324(+)
• Located in intron of: ENSCJAG00000001505

Retrocopy information

• Ensembl ID: ENSCJAG00000001551
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000001431
• Aliases: None
• Description: None

Sequence

>retro_cjac_2542
GGTTTTAAAGCCAACTTCTCTCTCTTGAGGAGGCCTGGAGAGAAAACTTACACACAGTGATGTCGGTTATTTGTTGGGAA
TCTACCTGCTGATATCACGGAAGATGAATTCAGAAGACTATTTGTTAAATATGGAGAACCTGGAAAAGATTTAATCAACA
AAGGCAAAGGATTCGGATTTATTAAGCCTGAATCCAGAGCTTTGGCTGAAATTGCCAAAGCTGAGCTCGATGATACGCCC
ATGAGAGGTAGACAGCTTCGAGTTCGCTTTGCCACACATGCTGCTGCCCTTTCTGTTCATAATCTTTCACCTTACGTTTC
CAATGAACTGTTGGAAGAAGCCTTCAGCCAGTTTGGTCCTATTGAAAGGGCTGTTGTAATAGTGGATGATCGTGGAAGAT
CTACAGGGAAAGGCATTGTTGAATTTGCTTCTAAACCAGCAGCAAGAAAGGCATTTGAACGATACAGTGAAGATGTTTTC
TTGCTGACAACAACTCCTCGTCCAGTCATCGTGGAACCACTTGAACAGCTAGCTGATGAAGATGGTCTTCCTGAAAAACT
TGCGCAGAAGAATCCGATGTATCAAAAGGAGAGAGAAACTCCTCGTTTTGCCCAGCATGGCACATTTGAGTACGAATATT
CTCAGCGATGGAAGTCGTTGGATGAAATGGAAAAACAGCAAAGAGAACAAATGAAAAAAATATGAAGGATGCAAAAGACA
AATTGGAAAGTGAAATGGAAGATGCCTATCATGAACATAGGCAAATCTTTTGCACCAAGATCTGATGAGACAACAGGAAG
AATTAAGACGCATGGAAGAACTTCATAATCAAGAAATGCAGAAACGTAAAGAAATGCAATTGAGGCAAGAGGAGGAACTA
CATAGAAGAGAGGAAGAGATGATGATTCGTCAGCGTGAGATGAAAGAACAAATGAGGCGCCAAAGAGAGGAAAGTTATAG
CCGAATGGGCTACATGGATCCAAGAGAAAGAGACATGAGAATGGGTGGCGGAGGAGCAATGAACATGGGAGATCCCTATG
GTTCAGGAGGCCAGAAATTTCCACCTCTAGGTGGTGGTGGTGGTGGCATAGGTTATGAAGCTAATCCTGGAGTTCCACCA
GCAACCATGAGTGGTTCCATGATAGGAAGTGACATGCGTACTGAGCACTTTGGGCAGGGAGGTGCGGGGCCTGTGGGTAG
ACAGGGTCCTAGAGGAATGGGGCCTGGAACTCCAGCAGGATATGGTAGAGGGAGAGAAGAGTACGAAGGCCCAAACAGAA
AAACCCCGATTT

Alignment

ORF - retro_cjac_2542 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.33 %
• Parental protein coverage: 93.29 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GFKANLSLLRRPGEKTYTQRCRLFVGNLPADITEDEFKRLFAKYGEPGEVFINKGKGFGFIKLESRALAE
          GFKAN.SLLRRPGEKTYTQ.CRLFVGNLPADITEDEF.RLF.KYGEPG...INKGKGFGFIK.ESRALAE
Retrocopy GFKANFSLLRRPGEKTYTQ*CRLFVGNLPADITEDEFRRLFVKYGEPGKDLINKGKGFGFIKPESRALAE

Parental  IAKAELDDTPMRGRQLRVRFATHAAALSVRNLSPYVSNELLEEAFSQFGPIERAVVIVDDRGRSTGKGIV
          IAKAELDDTPMRGRQLRVRFATHAAALSV.NLSPYVSNELLEEAFSQFGPIERAVVIVDDRGRSTGKGIV
Retrocopy IAKAELDDTPMRGRQLRVRFATHAAALSVHNLSPYVSNELLEEAFSQFGPIERAVVIVDDRGRSTGKGIV

Parental  EFASKPAARKAFERCSEGVFLLTTTPRPVIVEPLEQLDDEDGLPEKLAQKNPMYQKERETPPRFAQHGTF
          EFASKPAARKAFER.SE.VFLLTTTPRPVIVEPLEQL.DEDGLPEKLAQKNPMYQKERET.PRFAQHGTF
Retrocopy EFASKPAARKAFERYSEDVFLLTTTPRPVIVEPLEQLADEDGLPEKLAQKNPMYQKERET-PRFAQHGTF

Parental  EYEYSQRWKSLDEMEKQQREQV-EKNMKDAKDKLESEMEDAYHEHQ-ANLLRQDLMRRQEELRRMEELHN
          EYEYSQRWKSLDEMEKQQREQ..EKNMKDAKDKLESEMEDAYHEH..ANLL.QDLMR.QEELRRMEELHN
Retrocopy EYEYSQRWKSLDEMEKQQREQM<EKNMKDAKDKLESEMEDAYHEHR<ANLLHQDLMRQQEELRRMEELHN

Parental  QEMQKRKEMQLRQEEERRRREEEMMIRQREMEEQMRRQREESYSRMGYMDPRERDMTMGGGGAMNMGDPY
          QEMQKRKEMQLRQEEE..RREEEMMIRQREM.EQMRRQREESYSRMGYMDPRERDM.MGGGGAMNMGDPY
Retrocopy QEMQKRKEMQLRQEEELHRREEEMMIRQREMKEQMRRQREESYSRMGYMDPRERDMRMGGGGAMNMGDPY

Parental  GSGGQKFPPL-GGGGGIGYEANPGVPPATMSGSMMGSDMRTERFGQGGAGPVGGQGPRGMGPGTPAGYGR
          GSGGQKFPPL.GGGGGIGYEANPGVPPATMSGSM.GSDMRTE.FGQGGAGPVG.QGPRGMGPGTPAGYGR
Retrocopy GSGGQKFPPLGGGGGGIGYEANPGVPPATMSGSMIGSDMRTEHFGQGGAGPVGRQGPRGMGPGTPAGYGR

Parental  GREEYEGPNK-KPRF
          GREEYEGPN..KPRF
Retrocopy GREEYEGPNR>KPRF

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	8.61 RPM	53.03 RPM
SRP051959_heart	7.07 RPM	57.15 RPM
SRP051959_kidney	8.74 RPM	64.63 RPM
SRP051959_liver	4.27 RPM	35.29 RPM
SRP051959_lung	9.68 RPM	64.50 RPM
SRP051959_lymph_node	11.30 RPM	74.06 RPM
SRP051959_skeletal_muscle	5.90 RPM	38.28 RPM
SRP051959_spleen	9.58 RPM	63.68 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2542 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2542 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2542 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003595	1 retrocopy	retro_cfam_198,
Callithrix jacchus	ENSCJAG00000001431	4 retrocopies	retro_cjac_1073, retro_cjac_2542 , retro_cjac_2697, retro_cjac_486,
Callithrix jacchus	ENSCJAG00000036744	1 retrocopy	retro_cjac_3990,
Felis catus	ENSFCAG00000031287	1 retrocopy	retro_fcat_1989,
Gasterosteus aculeatus	ENSGACG00000002034	1 retrocopy	retro_gacu_13,
Gadus morhua	ENSGMOG00000011950	1 retrocopy	retro_gmor_20,
Macropus eugenii	ENSMEUG00000014082	1 retrocopy	retro_meug_164,
Oryctolagus cuniculus	ENSOCUG00000001877	1 retrocopy	retro_ocun_1834,
Oreochromis niloticus	ENSONIG00000017737	1 retrocopy	retro_onil_21,
Sarcophilus harrisii	ENSSHAG00000016107	1 retrocopy	retro_shar_36,
Tetraodon nigroviridis	ENSTNIG00000011331	1 retrocopy	retro_tnig_32,
Takifugu rubripes	ENSTRUG00000003783	1 retrocopy	retro_trub_8,
Drosophila melanogaster	FBgn0004227	1 retrocopy	retro_dmel_11,