RetrogeneDB ID: retro_cjac_2998

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:86040342..86041107(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BLMH
• Ensembl ID: ENSCJAG00000013781
• Aliases: None
• Description: bleomycin hydrolase [Source:HGNC Symbol;Acc:1059]

Sequence

>retro_cjac_2998
CTGAAGCTGGCCACAGTGCAGCGCACGCAGCAGGCATTCCAGGACACCATGCCCCAGGAAGGCAAGCCCGTCACCAAGCA
GAAGAGCTCAGGGCGATGTCTTTCCTTGTCTGAATGTAATGAGGCTTCCATTTGTGAAAAAATTAAATATTGGAGGATTT
GAGTTTAGTCAATCTTACCTGTTTTTTGGGGACAAGGTTGAATGCTGTTATTTCCTCTCAAATGCTTTTGTGGAGGCAGC
CCAGAGAAAAGAGCCTGAGGATGGGAGACTGGTGCAGTGTTTGCTTATGAACCCTGGAAATGATGGTGGCCAATGGGATA
TACTTGTCAATAGAGTTGCAAAATATGGTGTTATCCTTAATAAATGCTTCCCTGAATCTTATAGAACAGAGGCAACCAGA
AGGATGAATGATACTCGAATCACAAGATGAGTTAATTCTGTATACAACTATGGAACCTGGTACACAGTGGAGCCACCATA
GGAGCCACACAGGATGCTGTGATGAAGATGTTCCCAGTGGTGTGTTTCTGTTTGGGTGATCCACCAGACATTCACCTGGG
AGTATCAAGACAAAGATAAAAATTATCAGAAGATTGGCCCCACAATACCCTTGGAGTTTTACAGGGAACATGTCAAGCCA
CTCTTCAACATGGAAGATAAGATTTGTTTGGTGAATGACCCTAGGCCCAGCACAAGTACAACAAACTTCACACAGTGGAA
TACTTAAGCAATATGGTTGGAGGGAGAAAAACTCTATACAACAAC

Alignment

ORF - retro_cjac_2998 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.04 %
• Parental protein coverage: 57.74 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LKRATVQRAQHVFQHAVPQEGK-PVTNQKSSGRCWIFSCLNVMRLPFMKKLNIEEFEFSQSYLFFWDKVE
          LK.ATVQR.Q..FQ...PQEGK.P.......G....F.CLNVMRLPF.KKLNI..FEFSQSYLFF.DKVE
Retrocopy LKLATVQRTQQAFQDTMPQEGK>PSPSRRAQGD--VFPCLNVMRLPFVKKLNIGGFEFSQSYLFFGDKVE

Parental  RCYFFLNAFVDTAQRKEPEDGRLVQYLLMNPANDGGQWDMLVNIVEKYGVIPKKCFPESYTTEAT-RMND
          .CYF..NAFV..AQRKEPEDGRLVQ.LLMNP.NDGGQWD.LVN.V.KYGVI..KCFPESY.TEAT.RMND
Retrocopy CCYFLSNAFVEAAQRKEPEDGRLVQCLLMNPGNDGGQWDILVNRVAKYGVILNKCFPESYRTEATRRMND

Parental  -ILNPKMREFCIRLRNLVHSGATKGEISATQDGMMEEIFRVVCICLGNPPETFTWEYRD-KDKNYQKIGP
          ...N.KM..FCI.L.NLVHSGAT...I.ATQD..M...F.VVC.CLG.PP.......R..K.K......P
Retrocopy <YSNHKMS*FCIQLWNLVHSGAT---IGATQDAVM-KMFPVVCFCLGDPPDIHLGVSRQ<KIKIIRRLAP

Parental  -VTPLEFYREHVKPLFNMEAKICLVNDPRP-QHKYNKLYTVEYLSNMVGGRKTLYNN
          ...PLEFYREHVKPLFNME.KICLVNDPRP.QHKYNKL.TVEYLSNMVGGRKTLYNN
Retrocopy <TIPLEFYREHVKPLFNMEDKICLVNDPRP<QHKYNKLHTVEYLSNMVGGRKTLYNN

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	15.55 RPM
SRP051959_heart	0.00 RPM	12.37 RPM
SRP051959_kidney	0.00 RPM	21.19 RPM
SRP051959_liver	0.00 RPM	17.76 RPM
SRP051959_lung	0.00 RPM	16.23 RPM
SRP051959_lymph_node	0.00 RPM	17.76 RPM
SRP051959_skeletal_muscle	0.00 RPM	17.62 RPM
SRP051959_spleen	0.00 RPM	16.20 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2998 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2998 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2998 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021370	1 retrocopy	retro_btau_1510,
Callithrix jacchus	ENSCJAG00000013781	1 retrocopy	retro_cjac_2998 ,
Cavia porcellus	ENSCPOG00000005048	1 retrocopy	retro_cpor_896,
Macropus eugenii	ENSMEUG00000008938	1 retrocopy	retro_meug_2120,
Rattus norvegicus	ENSRNOG00000003563	1 retrocopy	retro_rnor_566,
Tursiops truncatus	ENSTTRG00000016341	1 retrocopy	retro_ttru_1915,
Vicugna pacos	ENSVPAG00000003571	1 retrocopy	retro_vpac_74,