RetrogeneDB ID: retro_cjac_3015

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:115938860..115939829(-)
• 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_3015
TCCAACATGGCAGGCAAATAGCTGTGTAATGAGTCCCACAAAGATAGAAAGAACTAGTCCACCCCCCCGCCCCCCAGCAT
TAGTGTGGTTGACAAGAAAGAGGAGACACAGCTGCCCATCATGCTTAAGAAAGAAGGTATAAGATGAGTTGGAAAGAGAC
CTGATCAACAACTTCAGGTTGAAGGGAAATAATTAATAGAAGACCAGAAACATGATCACCTCTAAAACAAAGATTTGAAA
AGCCAATTGAAGGAAAGAGTGGAGCAAATTTTCAGTTGAATAGACCGATTATTGACTGACATATTTGAGGCCATGGTGGT
CTTGGAAGAGGTCAAGGGGCCTGTGGGCATGGAATGGGTCGAGGAGATGGATTTGATTCCCATGGCATATGTGAATTTTA
TAGGCATAGTGGAAGTGATAGATCTGGCCTGAAGCACGAGGACAAACATGGAGTCACAGATCTCATTACTGTGGAACTGT
TAAAGATGAATTAATTGATTTGGATCAATCAAATGTGATTGTGGAACACCTGTAGGTGAAGAATATCCAATGGCAGACAC
TGAAAATAAGGAGAATGAAGTTGAAGAGTTAAAGGAAGAGGGTCCTAAAGAGATGACATTGGACGTGAAGACTATTCAAA
ATAAGGAGTGGGCAAAAGTGGAATTTAATATCTGAAAACCAAATGAGGCTGCTGAAGGCAGTGGGAAGAGGAAATTTGTT
TTTCATAAATCAAAGATTGAAGAAGCTTATGTTCCAGATTCTGTTATGGACTATCTTTTTCAAAAGCCAGCAAATGAGTA
ATATGTCAGTTGGAGATTAATTTTGGAGAACTTGGCTGCCCAGAACCTGATGGTGAGGGAGGACAAGGTGAATGTGGGTG
TGGCAGATGTCTGAACTGTGGCAGCAGAACTGACAAGTGAAGTGCTTCTGCTCCTCATGAGGATTAACCCAGAGGTATTC
CCAGATCTG

Alignment

ORF - retro_cjac_3015 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.17 %
• Parental protein coverage: 83.72 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  SNAAGKQLRKESQKDRKN---PLPPSVGVVDKKEETQPPVALKKEGIRRVGRRPDQQLQGEGK-IIDRRP
          SN.AGK.L..ES.KDRKN...P.PPS..VVDKKEETQ.P..LKKEGIR.VG.RPDQQLQ.EGK.II.RRP
Retrocopy SNMAGK*LCNESHKDRKN*STPPPPSISVVDKKEETQLPIMLKKEGIR*VGKRPDQQLQVEGK<IINRRP

Parental  ERRPPRERRFEKPLEEKGEGGEFSVDRPIIDRPIRGRGGLGRGRGGRGRGMGRGDGFDSRGKREFDRHSG
          E...P...RFEKP.E.K..G..F...RPIID..I.G.GGLGRG.G..G.GMGRGDGFDS.G..EF.RHSG
Retrocopy ET*SPLKQRFEKPIEGKS-GANFQLNRPIID*HI*GHGGLGRGQGACGHGMGRGDGFDSHGICEFYRHSG

Parental  SDRSGLKHEDKRG-GSGSHNWGTVKDELTDLEQSNVTEE-TPEGEEHHPVADTENKENEVEEVKEEGPKE
          SDRSGLKHEDK.G....SH..GTVKDEL.DL.QSNV..E.TP.GEE..P.ADTENKENEVEE.KEEGPKE
Retrocopy SDRSGLKHEDKHG<SHRSHYCGTVKDELIDLDQSNVIVE<TPVGEE-YPMADTENKENEVEELKEEGPKE

Parental  MTLDEWKAIQNKDRAKVEFNIRKPNEGADGQWKKGFVLHKSKSEEAHAEDSVMDHHFRKPAND-ITSQLE
          MTLD..K.IQNK..AKVEFNI.KPNE.A.G..K..FV.HKSK.EEA...DSVMD..F.KPAN.....QLE
Retrocopy MTLDV-KTIQNKEWAKVEFNI*KPNEAAEGSGKRKFVFHKSKIEEAYVPDSVMDYLFQKPANE<VICQLE

Parental  INFGDLGRPGRGGRGGRGGRGRGGRPNRGSRTDKSSASAPDVD-DPEAFPAL
          INFG.LG.P...G.GG.G..G.G...N.GSRTDK.SASAP..D..PE.FP.L
Retrocopy INFGELGCPEPDGEGGQGECGCGRCLNCGSRTDK*SASAPHED>NPEVFPDL

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	0.00 RPM	78.25 RPM
SRP051959_kidney	0.00 RPM	75.46 RPM
SRP051959_liver	0.00 RPM	100.79 RPM
SRP051959_lung	0.00 RPM	87.11 RPM
SRP051959_lymph_node	0.00 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_3015 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3015 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3015 has 0 orthologous retrocopies within eutheria group .

---

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,