RetrogeneDB ID: retro_cjac_2575

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:142829463..142830342(+)
• Located in intron of: ENSCJAG00000019517

Retrocopy information

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

Parental gene information

• Parental gene symbol: CIAPIN1
• Ensembl ID: ENSCJAG00000012055
• Aliases: CIAPIN1, anamorsin
• Description: cytokine induced apoptosis inhibitor 1 [Source:HGNC Symbol;Acc:28050]

Sequence

>retro_cjac_2575
AGTCATCCTCAGTGGAAACTGAAAGATCTGGTGGATAAGCTTCAAGTGTTAACTGGCAATGAAGCCTGCGTGTCTGTGGA
AAACATCAACCAGCTATTACAGTCTGCCCACAAGGAATCCAGCTTTGACATTATTCTGTCGGGTTTAGTCCCAGGAAGCA
CCACTCTGCACAGTGCTGAGCTTTTGGCTGAAATTGCCCAGATCCTTCGGCCTGGTGGATGTCTTTTTCTGAAGGGGCCA
GTAGAGACAGCTGTAGATAACAATACCTAAGTGAAGACAGCATCTAAGCTATGTTCAGCCCTGACTCTTTCTGGTCTTGT
GGAAGTGAAAGAGGTGCAGCAGGAGCCCTTAAGCCCCGAGGAAGTACAGTCTGTTTGAGAATGCCTGGGTCATGAAAGTG
ACAGCCTACTGTTTGTTCAGATTACAGGCAAAAAACCATACTTTGAAGTGGGTTCTCCTAGTCAGCTTCAGCTTTCCATC
ACCAAGAAGTCATCTCCTTCAGTGAAGCCTGCTGTGGACCCTGCTGCCAAGCTGGGGACACTCTCAGCCAATGATATGGA
GGACGACAGCATGGATCTCACTGACTCAGATGAGCTGCTGGGTCCAGAAGATTTGAAGAAGCCAGATACGGCTTCCCTGC
GGGCTGCTGCTTGTGGGGAAGGGAAAAAGAGGAAGGCCTGCAAGAACTGCCCCTGTGGCCTTGCTGAAGAACTGGAAAAA
GAGAAGTCAAGGGAATAGATGAGCTCCCAACCCAAGTTGGCTTGTGGAAACTGCTACCTGGGTGATGCCTTCCACTGTGC
CAGCTGCCCCTATCTTGGGGTGCCAGCCTTCAAACCTGGGGAAAAGGTGCTTCTAAGCGATAGCAATCTTCACGATGCC

Alignment

ORF - retro_cjac_2575 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.81 %
• Parental protein coverage: 94.25 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SSPVEALKDLVDKLQVLTGNEGHVSVENINQLLQSAHKESSFDIILSGLVPGSTTLHSAEILAEIARILR
          S.P...LKDLVDKLQVLTGNE..VSVENINQLLQSAHKESSFDIILSGLVPGSTTLHSAE.LAEIA.ILR
Retrocopy SHPQWKLKDLVDKLQVLTGNEACVSVENINQLLQSAHKESSFDIILSGLVPGSTTLHSAELLAEIAQILR

Parental  PGGCLFLKEPVETAVADNNSKVKTASKLCSALTLSGLVEVKELQQEPLSPKEVQSVREHLGHESDSLLFV
          PGGCLFLK.PVETAV.DNN..VKTASKLCSALTLSGLVEVKE.QQEPLSP.EVQSV.E.LGHESDSLLFV
Retrocopy PGGCLFLKGPVETAV-DNNT*VKTASKLCSALTLSGLVEVKEVQQEPLSPEEVQSV*ECLGHESDSLLFV

Parental  QITGKKPNFEVGSSSQLKLSVAKKSSPSVKPAVDPAAAKLWTLSANDMEDDSMDLIDSDELLDPEDLKKP
          QITGKKP.FEVGS.SQL.LS..KKSSPSVKPAVDPAA.KL.TLSANDMEDDSMDL.DSDELL.PEDLKKP
Retrocopy QITGKKPYFEVGSPSQLQLSITKKSSPSVKPAVDPAA-KLGTLSANDMEDDSMDLTDSDELLGPEDLKKP

Parental  DPASLRAAACGERKKRKACKNCTCGLAEELEREKSREQMSSQPKSACGNCYLGDAFRCASCPYLGMPAFK
          D.ASLRAAACGE.KKRKACKNC.CGLAEELE.EKSRE.MSSQPK.ACGNCYLGDAF.CASCPYLG.PAFK
Retrocopy DTASLRAAACGEGKKRKACKNCPCGLAEELEKEKSRE*MSSQPKLACGNCYLGDAFHCASCPYLGVPAFK

Parental  PGEKVLLSDSNLHDA
          PGEKVLLSDSNLHDA
Retrocopy PGEKVLLSDSNLHDA

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	0.64 RPM	10.43 RPM
SRP051959_heart	0.58 RPM	9.09 RPM
SRP051959_kidney	0.69 RPM	12.54 RPM
SRP051959_liver	0.74 RPM	7.19 RPM
SRP051959_lung	1.32 RPM	8.62 RPM
SRP051959_lymph_node	0.73 RPM	8.49 RPM
SRP051959_skeletal_muscle	0.35 RPM	10.11 RPM
SRP051959_spleen	0.71 RPM	7.58 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2575 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2575 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2575 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012055	1 retrocopy	retro_cjac_2575 ,
Homo sapiens	ENSG00000005194	1 retrocopy	retro_hsap_1875,
Gorilla gorilla	ENSGGOG00000012402	1 retrocopy	retro_ggor_1372,
Macaca mulatta	ENSMMUG00000020472	1 retrocopy	retro_mmul_1719,
Monodelphis domestica	ENSMODG00000013522	1 retrocopy	retro_mdom_456,
Nomascus leucogenys	ENSNLEG00000002876	1 retrocopy	retro_nleu_1229,
Pongo abelii	ENSPPYG00000007388	2 retrocopies	retro_pabe_1260, retro_pabe_1556,
Pan troglodytes	ENSPTRG00000008155	1 retrocopy	retro_ptro_1258,