RetrogeneDB ID: retro_cjac_1116

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 13:96935542..96935863(+)
• Located in intron of: ENSCJAG00000034578

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLIRP
• Ensembl ID: ENSCJAG00000016946
• Aliases: None
• Description: SRA stem-loop interacting RNA binding protein [Source:HGNC Symbol;Acc:20495]

Sequence

>retro_cjac_1116
ATGGTGGCCTTAGCAGTGAGTGGTGCTGTGGCGCTGTGTAGAAATACCAGCTGGCCAATTGCTCTTGTGAGAAGAATGCC
TTGCACCATGGCATTGAGTCAGCTGAGAGAACACTTTGCACAGTTTGGCCATATAACAAAGTGTATTGTACATTTTGACA
AGGAGGTTGGTTTTGACTGAGATTTAGGTTGGGTTCACTTTTCTTCAGAAGAACTTCAGAAGGCACTACAACAGGAAAAT
CATATTAGAGATGGAGTGAAGCTCCAGGTTCAAGCTCAAAGACCAAAAGTTTTGTGAAGATCTGATGAAAAGAAAGATTT
T

Alignment

ORF - retro_cjac_1116 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.3 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAALTATGAVALRRNVSRPVAFVRKIPWTAASSQLREHFAQFGHIKRCIVPFDKETGFHRGMGWVQFSSE
          M.AL...GAVAL.RN.S.P.A.VR..P.T.A.SQLREHFAQFGHI..CIV.FDKE.GF....GWV.FSS.
Retrocopy MVALAVSGAVALCRNTSWPIALVRRMPCTMALSQLREHFAQFGHITKCIVHFDKEVGFD*DLGWVHFSS-

Parental  EELQNALQQENHIIDGVKLQVQAQRPKILQIPDEEKDF
          EELQ.ALQQENHI.DGVKLQVQAQRPK.L...DE.KDF
Retrocopy EELQKALQQENHIRDGVKLQVQAQRPKVL*RSDEKKDF

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	0.02 RPM	7.65 RPM
SRP051959_heart	0.00 RPM	16.87 RPM
SRP051959_kidney	0.00 RPM	12.96 RPM
SRP051959_liver	0.00 RPM	12.50 RPM
SRP051959_lung	0.00 RPM	10.22 RPM
SRP051959_lymph_node	0.00 RPM	9.61 RPM
SRP051959_skeletal_muscle	0.00 RPM	18.76 RPM
SRP051959_spleen	0.00 RPM	9.75 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1116 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1116 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1116 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003975	3 retrocopies	retro_amel_307, retro_amel_326, retro_amel_340,
Bos taurus	ENSBTAG00000008135	3 retrocopies	retro_btau_1439, retro_btau_430, retro_btau_999,
Canis familiaris	ENSCAFG00000017230	1 retrocopy	retro_cfam_1303,
Callithrix jacchus	ENSCJAG00000016946	4 retrocopies	retro_cjac_1116 , retro_cjac_1307, retro_cjac_3298, retro_cjac_4132,
Cavia porcellus	ENSCPOG00000001500	2 retrocopies	retro_cpor_1388, retro_cpor_579,
Dasypus novemcinctus	ENSDNOG00000007721	3 retrocopies	retro_dnov_1721, retro_dnov_2460, retro_dnov_612,
Echinops telfairi	ENSETEG00000010345	4 retrocopies	retro_etel_1095, retro_etel_1277, retro_etel_1471, retro_etel_1792,
Felis catus	ENSFCAG00000024050	2 retrocopies	retro_fcat_1696, retro_fcat_695,
Homo sapiens	ENSG00000119705	1 retrocopy	retro_hsap_4769,
Gorilla gorilla	ENSGGOG00000011059	1 retrocopy	retro_ggor_2972,
Microcebus murinus	ENSMICG00000012080	3 retrocopies	retro_mmur_1254, retro_mmur_1504, retro_mmur_238,
Macaca mulatta	ENSMMUG00000029256	1 retrocopy	retro_mmul_2544,
Mus musculus	ENSMUSG00000021040	1 retrocopy	retro_mmus_1954,
Pongo abelii	ENSPPYG00000006030	1 retrocopy	retro_pabe_3712,
Pan troglodytes	ENSPTRG00000030691	1 retrocopy	retro_ptro_3176,
Rattus norvegicus	ENSRNOG00000012314	3 retrocopies	retro_rnor_1670, retro_rnor_749, retro_rnor_923,
Sus scrofa	ENSSSCG00000028167	5 retrocopies	retro_sscr_344, retro_sscr_345, retro_sscr_383, retro_sscr_384, retro_sscr_820,
Tupaia belangeri	ENSTBEG00000013979	2 retrocopies	retro_tbel_1146, retro_tbel_3713,
Vicugna pacos	ENSVPAG00000001781	2 retrocopies	retro_vpac_398, retro_vpac_418,