RetrogeneDB ID: retro_cjac_3305

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:54803281..54804028(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000014579
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ANP32A
• Ensembl ID: ENSCJAG00000002339
• Aliases: None
• Description: acidic (leucine-rich) nuclear phosphoprotein 32 family, member A [Source:HGNC Symbol;Acc:13233]

Sequence

>retro_cjac_3305
ATGGAGATGGGCAGACGGATTCATTTAGAGCTGCGGAACAGGACGCCCTCTGATGTGAAAGAACTTGTCCTGGACAACAG
TCGGTCGAATGAAGGCAAACTCGAAGGCCTCACAGATGAATTTGAAGAACTGGAATTCTTAAGTACAATCAACGTAGGCC
TCACCTCAATCGCAAACTTACCAAAGTTAAACAAACTTAAGAAGCTTGAACTAAGCGATAACAGAGTCTCAGGGGGCCTG
GAAGTATTGGCAGAAAAGTGTCCGAACCTCACACATCTAAATTTAAGTGGCAACAAAATTAAAGACCTCAGCACAATAGA
GCCACTGAAAAAGTTAGAAAACCTCAAGAGCTTAGACCTTTTCAATTGCGAGGTAACCAACCTGAATGACTATCGAGAAA
ACGTGTTCAAGCTCCTCCCGCAACTCACATATCTCGACGGCTATGACCGGGACGACAAGGAGGCCCCTGACTCGGATGCT
GAGGGCTACGTGGAGGGCCTGGATGATGAGGAGGAAGATGAGGATGAGGAGGAGTATGATGAAGATGCTCAGGTAGTGGA
AGACGAGGAGGACGAGGATGAGGAGGAGGAAGGTGAAGAGGAGGACGTGAGTGGAGAGGAGGAGGAGGATGAAGAAGGTT
ATAATGATGGAGAGGTAGATGACGAGGAAGATGAAGAAGAGCTTGGTGAAGAAGAAAGGGGTCAGAAGCGAAAACGAGAA
CCTGAAGTTGAGGGAGAAGATGACGAC

Alignment

ORF - retro_cjac_3305 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.77 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEMGRRIHLELRNRTPSDVKELVLDNSRSNEGKLEGLTDEFEELEFLSTINVGLTSIANLPKLNKLKKLE
          MEMGRRIHLELRNRTPSDVKELVLDNSRSNEGKLEGLTDEFEELEFLSTINVGLTSIANLPKLNKLKKLE
Retrocopy MEMGRRIHLELRNRTPSDVKELVLDNSRSNEGKLEGLTDEFEELEFLSTINVGLTSIANLPKLNKLKKLE

Parental  LSDNRVSGGLEVLAEKCPNLTHLNLSGNKIKDLSTIEPLKKLENLKSLDLFNCEVTNLNDYRENVFKLLP
          LSDNRVSGGLEVLAEKCPNLTHLNLSGNKIKDLSTIEPLKKLENLKSLDLFNCEVTNLNDYRENVFKLLP
Retrocopy LSDNRVSGGLEVLAEKCPNLTHLNLSGNKIKDLSTIEPLKKLENLKSLDLFNCEVTNLNDYRENVFKLLP

Parental  QLTYLDGYDRDDKEAPDSDAEGYVEGLDDEEEDEDEEEYDEDAQVVEDEEDEDEEEEGEEEDVSGEEEED
          QLTYLDGYDRDDKEAPDSDAEGYVEG.................QVVEDEEDEDEEEEGEEEDVSGEEEED
Retrocopy QLTYLDGYDRDDKEAPDSDAEGYVEGXXXXXXXXXXXXXXXXXQVVEDEEDEDEEEEGEEEDVSGEEEED

Parental  EEGYNDGEVDDEEDEEELGEEERGQKRKREPEDEGEDDD
          EEGYNDGEVDDEEDEEELGEEERGQKRKREPE.EGEDDD
Retrocopy EEGYNDGEVDDEEDEEELGEEERGQKRKREPEVEGEDDD

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	0.67 RPM	12.67 RPM
SRP051959_heart	0.96 RPM	24.21 RPM
SRP051959_kidney	0.89 RPM	22.34 RPM
SRP051959_liver	0.58 RPM	10.14 RPM
SRP051959_lung	2.02 RPM	30.13 RPM
SRP051959_lymph_node	1.89 RPM	26.64 RPM
SRP051959_skeletal_muscle	0.63 RPM	13.58 RPM
SRP051959_spleen	1.95 RPM	23.40 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3305 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3305 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3305 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002339	2 retrocopies	retro_cjac_3305 , retro_cjac_3799,
Callithrix jacchus	ENSCJAG00000009710	1 retrocopy	retro_cjac_2926,
Dasypus novemcinctus	ENSDNOG00000015360	5 retrocopies	retro_dnov_1199, retro_dnov_1250, retro_dnov_1696, retro_dnov_836, retro_dnov_956,
Dipodomys ordii	ENSDORG00000008611	1 retrocopy	retro_dord_240,
Felis catus	ENSFCAG00000015773	1 retrocopy	retro_fcat_1188,
Homo sapiens	ENSG00000140350	3 retrocopies	retro_hsap_1479, retro_hsap_3117, retro_hsap_48,
Gorilla gorilla	ENSGGOG00000015417	1 retrocopy	retro_ggor_1134,
Loxodonta africana	ENSLAFG00000022560	1 retrocopy	retro_lafr_679,
Macaca mulatta	ENSMMUG00000022717	1 retrocopy	retro_mmul_1985,
Nomascus leucogenys	ENSNLEG00000013347	2 retrocopies	retro_nleu_15, retro_nleu_2383,
Otolemur garnettii	ENSOGAG00000003058	1 retrocopy	retro_ogar_2596,
Ochotona princeps	ENSOPRG00000015394	2 retrocopies	retro_opri_302, retro_opri_563,
Pongo abelii	ENSPPYG00000006595	2 retrocopies	retro_pabe_210, retro_pabe_2575,
Pan troglodytes	ENSPTRG00000007219	2 retrocopies	retro_ptro_2108, retro_ptro_758,
Rattus norvegicus	ENSRNOG00000045651	1 retrocopy	retro_rnor_1043,
Sarcophilus harrisii	ENSSHAG00000010906	1 retrocopy	retro_shar_540,
Tupaia belangeri	ENSTBEG00000016417	2 retrocopies	retro_tbel_4078, retro_tbel_4595,