RetrogeneDB ID: retro_cjac_1207

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:49875096..49876208(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SERBP1
• Ensembl ID: ENSCJAG00000017440
• Aliases: None
• Description: SERPINE1 mRNA binding protein 1 [Source:HGNC Symbol;Acc:17860]

Sequence

>retro_cjac_1207
GTCACCAACCAATTGGAACAGTTATTCAACACTTTTGAGGTGTTGAAGGCAGCAGAGAACAAGAAAAAAGAAGCCAGCGG
GGCGGCGTTGGGGACCCTGGTGCCAAGAGCGCAGCAGCTCAGGCCGCGGCGCAGACTAGCTCGAAGGCGGCAGGCAAGCA
GCTGCGCAGAGTCCCAGAAAGACCGCAAAAACCCACTGCCCCCCAGCGTCGCGTGGTTGACGAGAAAGAGGAGACTCCGC
CGCCTGTGGCGCTTAAGAAACGAAGGAATAAGACAAATTGGAAGAAGACCTGATCAATAACTTCGGGATGAAGGGAAAAT
AATTGATAGAAGACCGGAAAGGCGACCACCTCGTGAACGACGATTTGAAAATCCACTTGAAGAAAAGGGGGAAGGGTGCG
AATTTTCAGTTGATAGACCGATTATTGACCGACCTATTCAAGATCGTGGTGGTCTTGGAAGAGGTCAAGGGGGTCATGGA
CGTGGAATGGGCAGAGGAGATGGATTTGATTCTCGTGGCACACGTGAATTTGATAGGCATAGTGGAAGTGATAGATCTGG
CCTGAAGCGCGATGACAAAAGTGGAGGTAGCGGATCTCACAACTGGGGAACTGTCCAAGGCGAATCAACTGACTTGGATC
AATCAAATGCCACGGAGGAAACACCTGAAGTTGAAGAACATCATCCAGTGGCCAACACTGAAAATTAGGAGAATGAAGTT
GAAGAGGTAAAAGACGAGGGTCCAAAAGAGATGACTTTGGATGAGTGGAAGGCTATTCAAAATAAGGACCGGGCAAAGGT
AGAATTTAATATCCGAAAACCAAAGGAAGGTGCAGAAGGGCAGTGGAAGAAGGGATTAGTTCTTCATAAACAAAGAGTGA
AGAGGCTCATGCTGAAGATTTGGGTATGGACTCTCATTTCTGGAAGCCAGCAAATGATATAACATCTCAGCTAGAGATCA
ATTTTGGAGACCTTGGCAACCCAGGACATGGTGACAGCAGAGTACGAGGTGGACATGGGTGTGGTGGGCCCCCAAATCTT
GGCAACAGGGCCAACAGGTTAAGTGCTTCTGCTCCTGATGTGGATGACCCAGAGGCATTCCCAGCTCTGGCT

Alignment

ORF - retro_cjac_1207 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.16 %
• Parental protein coverage: 96.9 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VTNRFDQLFDDESDPFEVLKAAENKKKEAGG-GGVGGPGAKS-AAQAAAQTNSNAAGKQLRKESQKDRKN
          VTN...QLF......FEVLKAAENKKKEA.G.GGVG.PGAKS.AAQAAAQT.S.AAGKQLR.......K.
Retrocopy VTNQLEQLFNT----FEVLKAAENKKKEASG<GGVGDPGAKSAAAQAAAQTSSKAAGKQLRRVPERPQK-

Parental  PLPPSVGVVDKKEETQPPVALKK-EGIRRVGRRPDQQLQGEGKIIDRRPERRPPRERRFEKPLEEKGEGG
          P..P...VVD.KEET.PPVALKK.EGIR..GRRPDQ.L..EGKIIDRRPERRPPRERRFE.PLEEKGEG.
Retrocopy PTAPQRRVVDEKEETPPPVALKK>EGIRQIGRRPDQ*LRDEGKIIDRRPERRPPRERRFENPLEEKGEGC

Parental  EFSVDRPIIDRPIRGRGGLGRGRGGRGRGMGRGDGFDSRGKREFDRHSGSDRSGLKHEDKRGGSGSHNWG
          EFSVDRPIIDRPI..RGGLGRG.GG.GRGMGRGDGFDSRG.REFDRHSGSDRSGLK..DK.GGSGSHNWG
Retrocopy EFSVDRPIIDRPIQDRGGLGRGQGGHGRGMGRGDGFDSRGTREFDRHSGSDRSGLKRDDKSGGSGSHNWG

Parental  TVKDELTDLEQSNVTEETPEGEEHHPVADTENKENEVEEVKEEGPKEMTLDEWKAIQNKDRAKVEFNIRK
          TV..E.TDL.QSN.TEETPE.EEHHPVA.TEN.ENEVEEVK.EGPKEMTLDEWKAIQNKDRAKVEFNIRK
Retrocopy TVQGESTDLDQSNATEETPEVEEHHPVANTEN*ENEVEEVKDEGPKEMTLDEWKAIQNKDRAKVEFNIRK

Parental  PNEGADGQWKKGFVLHK-SKSEEAHAEDSVMDHHFRKPANDITSQLEINFGDLGRPGRGGRGGRGGRGRG
          P.EGA.GQWKKG.VLHK..KSEEAHAED..MD.HF.KPANDITSQLEINFGDLG.PG.G....RGG.G.G
Retrocopy PKEGAEGQWKKGLVLHK<TKSEEAHAEDLGMDSHFWKPANDITSQLEINFGDLGNPGHGDSRVRGGHGCG

Parental  GRPNRGSRTDKSSASAPDVDDPEAFPALA
          G.PN.G.R....SASAPDVDDPEAFPALA
Retrocopy GPPNLGNRANRLSASAPDVDDPEAFPALA

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	78.88 RPM
SRP051959_heart	0.02 RPM	78.25 RPM
SRP051959_kidney	0.02 RPM	75.46 RPM
SRP051959_liver	0.00 RPM	100.79 RPM
SRP051959_lung	0.00 RPM	87.11 RPM
SRP051959_lymph_node	0.05 RPM	93.65 RPM
SRP051959_skeletal_muscle	0.00 RPM	127.23 RPM
SRP051959_spleen	0.00 RPM	82.94 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1207 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1207 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1207 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018538	1 retrocopy	retro_cfam_546,
Callithrix jacchus	ENSCJAG00000017440	2 retrocopies	retro_cjac_1207 , retro_cjac_3015,
Homo sapiens	ENSG00000142864	3 retrocopies	retro_hsap_3056, retro_hsap_413, retro_hsap_4695,
Gorilla gorilla	ENSGGOG00000010396	1 retrocopy	retro_ggor_408,
Myotis lucifugus	ENSMLUG00000001424	1 retrocopy	retro_mluc_691,
Oryctolagus cuniculus	ENSOCUG00000008946	1 retrocopy	retro_ocun_1041,
Otolemur garnettii	ENSOGAG00000025884	1 retrocopy	retro_ogar_185,
Pongo abelii	ENSPPYG00000001256	1 retrocopy	retro_pabe_3790,
Pan troglodytes	ENSPTRG00000023560	2 retrocopies	retro_ptro_1985, retro_ptro_317,
Sorex araneus	ENSSARG00000000803	1 retrocopy	retro_sara_135,
Tupaia belangeri	ENSTBEG00000003689	4 retrocopies	retro_tbel_1004, retro_tbel_1331, retro_tbel_2427, retro_tbel_532,