RetrogeneDB ID: retro_cjac_1073

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 13:18840132..18840950(+)
• Located in intron of: ENSCJAG00000014270

Retrocopy information

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

Parental gene information

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

Sequence

>retro_cjac_1073
CCCATGAGAGGTAGACAACTTAAAGTTTGTTTTGCCACACATGCCGCTGCCTTTTCTGTTTGTAATCTTTCACCTGATGT
TTCCAATGAACTGTTGGAAGAAGCCTTTAGCCAGTTTGGTCCTATTGAAAGGGCTGTTGTAATTGTGGATGATTGTGGAA
GATTCTATAGGGAAAGGCATTGTTGAATTTGCTTCTAAAGGAGCAGCAAGAAAGGCATTTGAACGATACAATGAAGGTAT
TTTCTTGCTGACAGCAACTCGTCCAGTCATTGTGGAACCACTTGAACAACTAGACTATTAGGATGGTCTTCCTGAAAAAC
TTGCATAGAAGAATCCAGTGCATCAGATGGAGAGAGAAACCCCTCTTCGTTTTGTCCAGCATGGCACATCTCAGTATGAA
TATTCTCAGCAATGGAAGTCCTAGGATGAAATTGAAAAACAGCAAAGGGAACAAGTAGAAAAAACATGAAGGATGCAAAA
GACAAATTGGAAAATGAAATGGGAGATGTCAATCATGAACATCAAGCAAACCTTTTACACCAAGATCTGATGAGACGACA
GGAAGAACTAAGACACATGGTAGAACTTCACAATCAAGAAATGCAGAAACGTAAAGAAATGTGAGGCAAGAGGAGGAACG
ATGTAGAAGACAGGAAGAGATGATTCATCAATGTGAGATGGAAGAACAAACAAGATCCCAAAGAGAGGAAAGTTACGGCC
AAGTGGGCTACATGGATCCGAAAGAAACAGACATGAGAATGGGTGGCGGAGGAGCAGTGAACATGGGAGATCCCTATGAT
TCAGGAGGCCAAACATTT

Alignment

ORF - retro_cjac_1073 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.21 %
• Parental protein coverage: 59.74 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PMRGRQLRVRFATHAAALSVRNLSPYVSNELLEEAFSQFGPIERAVVIVDDRGR-STGKGIVEFASKPAA
          PMRGRQL.V.FATHAAA.SV.NLSP.VSNELLEEAFSQFGPIERAVVIVDD.GR.S.GKGIVEFASK.AA
Retrocopy PMRGRQLKVCFATHAAAFSVCNLSPDVSNELLEEAFSQFGPIERAVVIVDDCGR>SIGKGIVEFASKGAA

Parental  RKAFERCSEGVFLLTTTPRPVIVEPLEQLDDEDGLPEKLAQKNPMYQKERETPPRFAQHGTFEYEYSQRW
          RKAFER..EG.FLLT.T.RPVIVEPLEQLD..DGLPEKLA.KNP..Q.ERETP.RF.QHGT..YEYSQ.W
Retrocopy RKAFERYNEGIFLLTAT-RPVIVEPLEQLDY*DGLPEKLA*KNPVHQMERETPLRFVQHGTSQYEYSQQW

Parental  KSLDEMEKQQREQVE-KNMKDAKDKLESEMEDAYHEHQANLLRQDLMRRQEELRRMEELHNQEMQKRKEM
          KS.DE.EKQQREQVE.KNMKDAKDKLE.EM.D..HEHQANLL.QDLMRRQEELR.M.ELHNQEMQKRKEM
Retrocopy KS*DEIEKQQREQVE<KNMKDAKDKLENEMGDVNHEHQANLLHQDLMRRQEELRHMVELHNQEMQKRKEM

Parental  -QLRQEEERRRREEEMMIRQREMEEQMRRQREESYSRMGYMDPRERDMTMGGGGAMNMGDPYGSGGQKF
          .....EE..RR.EE..MI.Q.EMEEQ.R.QREESY...GYMDP.E.DM.MGGGGA.NMGDPY.SGGQ.F
Retrocopy <VRQEEERCRRQEE--MIHQCEMEEQTRSQREESYGQVGYMDPKETDMRMGGGGAVNMGDPYDSGGQTF

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	0.13 RPM	53.03 RPM
SRP051959_heart	0.77 RPM	57.15 RPM
SRP051959_kidney	0.51 RPM	64.63 RPM
SRP051959_liver	0.13 RPM	35.29 RPM
SRP051959_lung	1.94 RPM	64.50 RPM
SRP051959_lymph_node	1.12 RPM	74.06 RPM
SRP051959_skeletal_muscle	0.20 RPM	38.28 RPM
SRP051959_spleen	0.55 RPM	63.68 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1073 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1073 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1073 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,