RetrogeneDB ID: retro_cjac_1574

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 17:70204121..70204756(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEC13
• Ensembl ID: ENSCJAG00000016439
• Aliases: None
• Description: None

Sequence

>retro_cjac_1574
CTGGTGTCAGTAATTAACACTGTGGATCCCTCCCCTGAGGACATGATTCACGAAGCCCAGATGGACGACTACGGCACCCC
TCTGGCAACCTGCTCCTCAGACAGGTCCGTCCAAATCTTCAACGGAGGGCGATCCCCATCGCCGACCTCAGGGGTCATGG
CCATCCGTGTGGCAAGTGGTGTGGGCTCACCCCGTGTACAGCAACATCCCGGCATCATGCTCCTCTGACCGGAGAGTCAT
TATCTGGACACAGGAAAACAGCACCTGGGAGAAGAGCCACGAGCACGCGGGAGACGACTCCTCAATGAACCTGCCGTGCT
GGTCCCCCATGACTACGGCCTGATCCTGGCCTGTGGGAGCTCGGAAGGGGCCATCTCCCTGCTGACTTACACCGGGGAAG
ACCAGTGGGAAGTAAAGAAGACCAACAATGCTCACACCATTGGCTGAAATGCTGTCGAGGGGGGCCTCTGCTGTTGTAGC
TGGGAGCCTCAGAGCAGCCATCAGGGCAGAAACCCAATTACATCAAGAAGTTTGCATCAGGTGGCTGTGACAACCTCATC
TAGCTGTGGAAGGAGGAGGAGGGTGGCCAGTGGATGGGGGAGCAGAGGCTGGAATCGCACAGTGACTGGGTTCAA

Alignment

ORF - retro_cjac_1574 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.0 %
• Parental protein coverage: 62.97 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MVSVINTVDTSHEDMIHDAQMDYYGTRLATCSSDRSVKIFDVRNGGQ-ILIADLRGHEGP-VWQVAWAHP
          .VSVINTVD.S.EDMIH.AQMD.YGT.LATCSSDRSV.IF...NGG..I.IADLRGH..P.VWQV.WAHP
Retrocopy LVSVINTVDPSPEDMIHEAQMDDYGTPLATCSSDRSVQIF---NGGR<IPIADLRGHGHP<VWQVVWAHP

Parental  MYGNILASCSYDRKVIIWREENGTWEKSHEHAGHDSSVNSVCWAP-HDYGLILACGSSDGAISLLTYTGE
          .Y.NI.ASCS.DR.VIIW..EN.TWEKSHEHAG.DSS.N..CW.P.HDYGLILACGSS.GAISLLTYTGE
Retrocopy VYSNIPASCSSDRRVIIWTQENSTWEKSHEHAGDDSSMNLPCWSP<HDYGLILACGSSEGAISLLTYTGE

Parental  GQWEVKKINNAHTIGCNAVSWA-PAVVPGSLIDQPSGQKPNYIKKFASGGCDNLIKLWKEEEDGQWKEEQ
          .QWEVKK.NNAHTIG.NAV....P.........QPSGQKPNYIKKFASGGCDNLI.LWKEEE.GQW..EQ
Retrocopy DQWEVKKTNNAHTIG*NAVEGG<PLLL*LGASEQPSGQKPNYIKKFASGGCDNLI*LWKEEEGGQWMGEQ

Parental  KLEAHSDWVR
          .LE.HSDWV.
Retrocopy RLESHSDWVQ

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	16.00 RPM
SRP051959_heart	0.00 RPM	9.79 RPM
SRP051959_kidney	0.00 RPM	15.33 RPM
SRP051959_liver	0.00 RPM	17.85 RPM
SRP051959_lung	0.00 RPM	11.06 RPM
SRP051959_lymph_node	0.00 RPM	12.31 RPM
SRP051959_skeletal_muscle	0.00 RPM	11.33 RPM
SRP051959_spleen	0.00 RPM	13.93 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1574 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1574 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1574 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005118	1 retrocopy	retro_cfam_278,
Callithrix jacchus	ENSCJAG00000016439	2 retrocopies	retro_cjac_1574 , retro_cjac_908,
Felis catus	ENSFCAG00000011245	1 retrocopy	retro_fcat_541,
Homo sapiens	ENSG00000157020	1 retrocopy	retro_hsap_2630,
Microcebus murinus	ENSMICG00000002401	1 retrocopy	retro_mmur_1509,
Mus musculus	ENSMUSG00000030298	2 retrocopies	retro_mmus_2159, retro_mmus_3443,
Nomascus leucogenys	ENSNLEG00000004482	1 retrocopy	retro_nleu_642,
Otolemur garnettii	ENSOGAG00000017050	1 retrocopy	retro_ogar_1655,
Pongo abelii	ENSPPYG00000013658	1 retrocopy	retro_pabe_2333,
Pan troglodytes	ENSPTRG00000014619	1 retrocopy	retro_ptro_1774,
Rattus norvegicus	ENSRNOG00000010628	2 retrocopies	retro_rnor_1375, retro_rnor_1454,
Tursiops truncatus	ENSTTRG00000004395	1 retrocopy	retro_ttru_917,