RetrogeneDB ID: retro_cjac_2023

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 21:8300786..8301348(+)
• Located in intron of: ENSCJAG00000008885

Retrocopy information

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

Parental gene information

• Parental gene symbol: HEBP1
• Ensembl ID: ENSCJAG00000021628
• Aliases: None
• Description: heme binding protein 1 [Source:HGNC Symbol;Acc:17176]

Sequence

>retro_cjac_2023
ATGTGGGGCGTCATCAAGAACTCGCTATTCCGAAGCCTAGAGGCGTGGCCTTGGGAGACCCTAAGCCAAGGGGACAAGGA
AGAATCCTCCTAGGAGGGCCTGTGAAGGAGGCAAGTTTGCCACAGTAGAAGTGACAGAAAAGTCTGCGGATGTGCCTCTA
CCGGAAGCAATGCCCAAGGTCGCAAAGTACGCGGCGGGCACCAATGACAAGGAAATTAGGCCGAAGATGACGGTACCTAT
TTCCTTTGCCGCGTTCCCCAGTGAAGACGGCTCTCTGCAGCAGAAACTAAAAGTTTGGTTCCGGATTCCAAGCCCATTTC
AAAGCGGCCCACCAGCTGGCAGTGACAACAGCGTAGAGATTGAGGAACTGGAAGGCGTCACCGTCTGTTCCATGCAGTTT
CGGAGCTAGGCCAAGGAAGCAGACTACGGAGCGCACACCGCCTGGCTGCGAGCTGCCCTGGAGCGCAGAGCCACCTGCCG
GGGGGACATCTGCTTCTGCAGCTGTTCTGATCCTCCCGGGAAGCCCTGCGGACGGCGCAGTGAGATCTGGCTGCGGAAGT
CA

Alignment

ORF - retro_cjac_2023 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.42 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLGMIRNSLFGSVETWPWQVLS-KGDKEEVSYEERACEGGKFATVEVTDKPVDEALREAMPKVAKYAGGT
          M.G.I.NSLF.S.E.WPW..LS.KG.........RACEGGKFATVEVT.K..D..L.EAMPKVAKYA.GT
Retrocopy MWGVIKNSLFRSLEAWPWETLS>KGTRKNPP--RRACEGGKFATVEVTEKSADVPLPEAMPKVAKYAAGT

Parental  NDKGIGMGMTVPISFAVFPNEDGSLQKKLKVWFRIPNQFQSDPPAPSDKSVKIEEREGITVYSMQFGGYA
          NDK.I...MTVPISFA.FP.EDGSLQ.KLKVWFRIP..FQS.PPA.SD.SV.IEE.EG.TV.SMQF...A
Retrocopy NDKEIRPKMTVPISFAAFPSEDGSLQQKLKVWFRIPSPFQSGPPAGSDNSVEIEELEGVTVCSMQFRS*A

Parental  KEADYVAHASRLRAALEGTATCRGDVYFCTGYDPPMKPYGRRNEIWLLKT
          KEADY.AH...LRAALE..ATCRGD..FC...DPP.KP.GRR.EIWL.K.
Retrocopy KEADYGAHTAWLRAALERRATCRGDICFCSCSDPPGKPCGRRSEIWLRKS

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	3.71 RPM
SRP051959_heart	0.00 RPM	4.68 RPM
SRP051959_kidney	0.00 RPM	13.87 RPM
SRP051959_liver	0.00 RPM	30.87 RPM
SRP051959_lung	0.00 RPM	6.23 RPM
SRP051959_lymph_node	0.00 RPM	4.25 RPM
SRP051959_skeletal_muscle	0.02 RPM	1.57 RPM
SRP051959_spleen	0.00 RPM	17.35 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2023 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2023 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2023 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
Ailuropoda melanoleuca	ENSAMEG00000010728	1 retrocopy	retro_amel_1466,
Canis familiaris	ENSCAFG00000013209	1 retrocopy	retro_cfam_1082,
Callithrix jacchus	ENSCJAG00000019060	1 retrocopy	retro_cjac_2727,
Callithrix jacchus	ENSCJAG00000021628	1 retrocopy	retro_cjac_2023 ,
Mustela putorius furo	ENSMPUG00000011702	1 retrocopy	retro_mputfur_498,
Otolemur garnettii	ENSOGAG00000033976	1 retrocopy	retro_ogar_756,
Tarsius syrichta	ENSTSYG00000014555	1 retrocopy	retro_tsyr_2076,