RetrogeneDB ID: retro_cjac_2727

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:63181926..63182449(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HEBP2
• Ensembl ID: ENSCJAG00000019060
• Aliases: None
• Description: heme binding protein 2 [Source:HGNC Symbol;Acc:15716]

Sequence

>retro_cjac_2727
ACACTGGACTGGAAGGCCCCAGAGAATGCAAGCCCCCAACTCTGAAGTCATGGGATCCGACAATATGGACCTGCTAAGTG
GGTCAGCACTTCTGTTGAGTCTATGAACAGGGGTCCAGCCATCAAGACAGGCTTTACAAAACCGAATAGCTACATACAAG
GCAAAAGAAGAAAGAGATGAAAATAATGACAGCTTCAGTCACAAGCTACACAGACGTTGGTTCAGGTCTTTTAGTGAGTC
TACCACGTCCATGTCCCTGTACATCTCCTCTGAACAGCAATTTCATCTGCCCAGGCCTTCAGACTTTATTGAAGACACAG
TCAATATGATTGTGTTTCATTCAATCATTCTCTAGTGCCCCAAATAATCAAGAACAACTTTTGACATTAGCAAGGATTTT
GAAGGAAGAAGGAAAAGTTTTCAATAAAAGGTGTACTACACTGCAGACTACATCAGTCCTTCCAAATAGCTTAATAGAAA
TAATAAAGTGTAATTGATTCAGAAAAAGGAGTCCTCCAAGGAA

Alignment

ORF - retro_cjac_2727 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.05 %
• Parental protein coverage: 88.78 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  TPGWKAPDDAGPQPGSYEIRHYGPAKWVSTSVESMDWDSAIQTGFTKLNSYIQGK-NEKEMKIKMTAPVI
          T..WKAP..A.PQ..S..IR.YGPAKWVSTSVESM....AI.TGFTK.NSYIQGK...KEMKI.MTA.V.
Retrocopy TLDWKAPENASPQL*SHGIRQYGPAKWVSTSVESMNRGPAIKTGFTKPNSYIQGK<KKKEMKI-MTASVT

Parental  SYVVPGSG-PFSESTITISLYIPSEQQFDPPKPLESDVFIEDRAEMTV-FVRSFDGFSSAQKNQEQLLTL
          SY...GSG..FSEST...SLYI.SEQQF..P.P.....FIED...M.V.F..SF...SSA..NQEQLLTL
Retrocopy SYTDVGSG<SFSESTTSMSLYISSEQQFHLPRPSD---FIEDTVNMIV>FIQSF---SSAPNNQEQLLTL

Parental  ASILRENGKVFDE-KVYYTAGYNSPFKLLNRNNEVWLIQKREPSKE
          A.IL.E.GKVF...KVYYTA.Y.SP.K.LNRNN.V.LIQK.E.SKE
Retrocopy ARILKEEGKVFNK<KVYYTADYISPSK*LNRNNKV*LIQKKESSKE

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	3.68 RPM
SRP051959_heart	0.00 RPM	11.94 RPM
SRP051959_kidney	0.00 RPM	5.86 RPM
SRP051959_liver	0.00 RPM	1.86 RPM
SRP051959_lung	0.00 RPM	6.65 RPM
SRP051959_lymph_node	0.00 RPM	1.16 RPM
SRP051959_skeletal_muscle	0.00 RPM	1.57 RPM
SRP051959_spleen	0.00 RPM	1.55 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2727 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2727 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2727 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2333
Gorilla gorilla	retro_ggor_1770

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019060	1 retrocopy	retro_cjac_2727 ,
Callithrix jacchus	ENSCJAG00000021628	1 retrocopy	retro_cjac_2023,
Dasypus novemcinctus	ENSDNOG00000008868	1 retrocopy	retro_dnov_1268,
Echinops telfairi	ENSETEG00000009265	1 retrocopy	retro_etel_973,
Homo sapiens	ENSG00000051620	1 retrocopy	retro_hsap_2333,
Gorilla gorilla	ENSGGOG00000001584	1 retrocopy	retro_ggor_1770,
Loxodonta africana	ENSLAFG00000013501	1 retrocopy	retro_lafr_752,
Otolemur garnettii	ENSOGAG00000005010	1 retrocopy	retro_ogar_2762,