RetrogeneDB ID: retro_cjac_273

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:63148714..63149476(+)
• Located in intron of: ENSCJAG00000008438

Retrocopy information

• Ensembl ID: ENSCJAG00000022611
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PNO1
• Ensembl ID: ENSCJAG00000006564
• Aliases: None
• Description: RNA-binding protein PNO1 [Source:RefSeq peptide;Acc:NP_001257650]

Sequence

>retro_cjac_273
TTGGAATCCGAAATGGAAGCAGAGAGCACCGGGGCAGAGGAGGGCTTTACCCAGGTCACCTGCAAGGGTGGCCGGCGGGC
GAAAAAACGGCAGGCTGAACAGCTGTCCGCAGCGGGAGAGGGCAGGGATGTGGGCCTTATGGACACAGAAGAGGCCAGGT
CGGCAAAGAGGCCAGTCTTCCCGCCCCTCTGCGGTGACGGGCTCCTGACTGGGAAAGAAGAAACAAGGAAAATTCCGGTC
CCAGCTAACAGATACACACCATTAAAAGAAAACTGGTTGAAGATATTTACTCCTATTGTGGAACATTTGGGACTTCAGAT
ACGCTTTAACTTGAAATCAAGGAATGTAGAAATCAGGACTTGTAAAGAAACAAGGGATGTTAGTGCTCTGACAAAAGCAG
CTGATTTTGTGAAAGCCTTTATTCTTGGCTTTCAGGTGGAGGATGCACTTGCCCTCATCAGGTTGGATGACCTCTTCCTA
GAGTCTTTTGAAATTACAGTTGTTAAACCCTTAAAGGGAGACCATCTATCCAGGGCAATAGGAAGAATTGCTGGCAAAGG
AGGAAAAAACAAATTCACCATAGAGAATGTGACACGGACGCGGATAGTTTTGGCTGATGTCAAAGTTCACATCCTTGGCT
CCTTCCAAAACATCAAGATGGCAAAAACTGCCATTTGCAACCTAATCTTGGGAAATCCTCCTCCTGCCAAGGTTTATGGC
AATATTCGAGCTGTGGCTAGCAGATCAACAGATCGATTCTGA

Alignment

ORF - retro_cjac_273 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.07 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LESEMEAQSAGAEDGFTQVTRKGGRRAKKRQAEQLSAAGEGGDAGLMDTEEARPAKRPVFPPLCGDGLLS
          LESEMEA.S.GAE.GFTQVT.KGGRRAKKRQAEQLSAAGEG.D.GLMDTEEAR.AKRPVFPPLCGDGLL.
Retrocopy LESEMEAESTGAEEGFTQVTCKGGRRAKKRQAEQLSAAGEGRDVGLMDTEEARSAKRPVFPPLCGDGLLT

Parental  GKEETRKIPVPANRYTPLKENWMKIFTPIVEHLGLQIRFNLKSRNVEIRTCKETRDVSALTKAADFVKAF
          GKEETRKIPVPANRYTPLKENW.KIFTPIVEHLGLQIRFNLKSRNVEIRTCKETRDVSALTKAADFVKAF
Retrocopy GKEETRKIPVPANRYTPLKENWLKIFTPIVEHLGLQIRFNLKSRNVEIRTCKETRDVSALTKAADFVKAF

Parental  ILGFQVEDALALIRLDDLFLESFEITDVKPLKGDHLSRAIGRIAGKGGKTKFTIENVTRTRIVLADVKVH
          ILGFQVEDALALIRLDDLFLESFEIT.VKPLKGDHLSRAIGRIAGKGGK.KFTIENVTRTRIVLADVKVH
Retrocopy ILGFQVEDALALIRLDDLFLESFEITVVKPLKGDHLSRAIGRIAGKGGKNKFTIENVTRTRIVLADVKVH

Parental  ILGSFQNIKMARTAICNLILGN-PPSKVYGNIRAVASRSADRF
          ILGSFQNIKMA.TAICNLILGN.PP.KVYGNIRAVASRS.DRF
Retrocopy ILGSFQNIKMAKTAICNLILGNPPPAKVYGNIRAVASRSTDRF

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	0.62 RPM	8.30 RPM
SRP051959_heart	0.47 RPM	6.54 RPM
SRP051959_kidney	0.58 RPM	11.60 RPM
SRP051959_liver	0.71 RPM	8.86 RPM
SRP051959_lung	0.98 RPM	5.81 RPM
SRP051959_lymph_node	1.14 RPM	6.96 RPM
SRP051959_skeletal_muscle	0.44 RPM	8.87 RPM
SRP051959_spleen	1.58 RPM	7.52 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_273 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_273 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_273 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003256	1 retrocopy	retro_cfam_1886,
Callithrix jacchus	ENSCJAG00000006564	3 retrocopies	retro_cjac_2615, retro_cjac_273 , retro_cjac_4127,
Felis catus	ENSFCAG00000025330	2 retrocopies	retro_fcat_1521, retro_fcat_864,
Loxodonta africana	ENSLAFG00000000046	1 retrocopy	retro_lafr_419,
Microcebus murinus	ENSMICG00000010897	1 retrocopy	retro_mmur_516,
Myotis lucifugus	ENSMLUG00000010850	1 retrocopy	retro_mluc_1719,
Macaca mulatta	ENSMMUG00000017461	2 retrocopies	retro_mmul_102, retro_mmul_352,
Nomascus leucogenys	ENSNLEG00000009993	1 retrocopy	retro_nleu_2389,
Oryctolagus cuniculus	ENSOCUG00000006100	1 retrocopy	retro_ocun_47,
Otolemur garnettii	ENSOGAG00000016637	1 retrocopy	retro_ogar_3025,
Pongo abelii	ENSPPYG00000012353	1 retrocopy	retro_pabe_1232,
Rattus norvegicus	ENSRNOG00000005524	1 retrocopy	retro_rnor_712,
Sus scrofa	ENSSSCG00000008352	2 retrocopies	retro_sscr_114, retro_sscr_352,
Tarsius syrichta	ENSTSYG00000004007	1 retrocopy	retro_tsyr_1625,