RetrogeneDB ID: retro_cjac_3201

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:27414314..27415581(+)
• Located in intron of: ENSCJAG00000013333

Retrocopy information

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

Parental gene information

• Parental gene symbol: LSM14A
• Ensembl ID: ENSCJAG00000010360
• Aliases: None
• Description: LSM14A, SCD6 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:24489]

Sequence

>retro_cjac_3201
GGCACCCCTTACATCCGCAGCAAGATCAGCCTCATCTCCAAGGCGGAGATCTGCTACGAGAGCATCCTCTACACCGACAC
TGAAAACTCCACCTTAGCCCTCGCCAAAGTTCGATCCTTTGGTACAGAAGACAGACCAACAGATCGTCCAATACCACCTC
GAGATGAAGTCTTTGAATACATTATAATCCGTGGGAGTGACACTAAAGACCTCACTGTTCGTGAGCCACCAAAACCACAG
TGTTCTTCGCCTCAAGACCCAGCTACCGTTTAGTCAGTCCTCACTGGGCTCATCACTTCTTCATTCCAGTCCACGGGTTC
TTCTGGGCCTTTCGGCAGGATGCCCACATACAGTCAGTTCAGTCCAAGTTCCTTAGTTGGGCAGCTGTTTGGTGCTGCTG
TTATTGCTGAAGCTCTTTGACATCCTTTGGAACAGAAACATCGAACAGTGGTACCTTACCCCAAAGTACTGCAGTTGGTT
CTGCCTTTACACAGGATACAGGATCCCTAAAAACACGGTTATCTCAAGGTCGTTCAAGCCCTTAGTTAAACCCTTTGAGA
AAAAGCCCAACCATGGAACAAGCAGTGCAGACCACCTCGGCCCACTTACCTGCTCCAGCACCAGTTGGGAGAAGGAGTCC
TGTATCAACCAGGCCTTTGCCATCTACCAGCCAAAAAGCAACAGAGGAGCACAGCCGAGCTGAAGTACACAAAGTTTCAA
GGCCAGAAAATGAGCAATTCAGAAATGATAATAAGAGACAAGTAGCTCCAGGTGTTCCTTCAGCTCCAAGGAGAGGGCAT
GGGGGTCATCGGGGTGGCAAGGGAAGATCTGGTATTCAGCGAGATGGGCCAATGAAATTTGAGAAAGACTTTGACTTTAA
AAGTGCAAATGCACAATTCAACAAGGAAGAGATTGACAGAGAGTTTCATAATAAGCTTAAATTAAAAAAGATAAACTTGA
GAAACAGGAGAAGCCTGTAAATGGTGAAGATAAAGGAGACTCAGGAGTTGATACACAAAACAGTGAAGGAAATGCTGATG
AAGAAGATCCACTTGGACCTAATTGCTATTATGACAAAACTAAATCCTTCATTGATAATATTTCTTGTAATGACAATAGA
AAATGGAGACCAACCTGGGCTGAAGAAAGATTAAATGCTGAAACATTTGGAATCCCACTTCGTCCAAATCGTGATCGTGG
GGGATACCAAGGCAGAGGAGGTCTTGGTTTCTGTGGTGGCAGAGGATTCAGAGGAGGTCGTGGGGGT

Alignment

ORF - retro_cjac_3201 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.65 %
• Parental protein coverage: 92.01 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GTPYIGSKISLISKAEIRYEGILYTIDTENSPVALAKVRSFGTEDRPTDRPIPPRDEVFEYIIFRGSDIK
          GTPYI.SKISLISKAEI.YE.ILYT.DTENS..ALAKVRSFGTEDRPTDRPIPPRDEVFEYII.RGSD.K
Retrocopy GTPYIRSKISLISKAEICYESILYT-DTENSTLALAKVRSFGTEDRPTDRPIPPRDEVFEYIIIRGSDTK

Parental  DLTVCEPPKPQCSLPQDPAIVQSSL-GSSTSSFQSMGSYGPFGRMPTYSQFSPSSLVGQQFGAVGVAG-S
          DLTV.EPPKPQCS.PQDPA.V.S.L.G..TSSFQS.GS.GPFGRMPTYSQFSPSSLVGQ.FGA...A..S
Retrocopy DLTVREPPKPQCSSPQDPATV*SVLTGLITSSFQSTGSSGPFGRMPTYSQFSPSSLVGQLFGAAVIAE<S

Parental  SLTSFGTETSNSGTLPQSSAVGSAFTQDTRSLKTQLSQGRSSPQLDPLRKSPTMEQAVQTASAHLPAPAP
          SLTSFGTETSNSGTLPQS.AVGSAFTQDT.SLKT.LSQGRSSP.L.PLRKSPTMEQAVQT.SAHLPAPAP
Retrocopy SLTSFGTETSNSGTLPQSTAVGSAFTQDTGSLKTRLSQGRSSP*LNPLRKSPTMEQAVQTTSAHLPAPAP

Parental  VGRRSPVSTRPLPSTSQKAIENQEHRRAEVHKVSRPENEQLRNDNKRQVAPGAPSAPRRGRGGHRGGRGR
          VGRRSPVSTRPLPSTSQKA.E..EH.RAEVHKVSRPENEQ.RNDNKRQVAPG.PSAPRRG.GGHRGG.GR
Retrocopy VGRRSPVSTRPLPSTSQKATE--EHSRAEVHKVSRPENEQFRNDNKRQVAPGVPSAPRRGHGGHRGGKGR

Parental  FGIRRDGPMKFEKDFDFESANAQFNKEEIDREFHNKLKL-KEDKLEKQEKPVNGEDKGDSGVDTQNSEGN
          .GI.RDGPMKFEKDFDF.SANAQFNKEEIDREFHNKLKL.K.DKLEKQEKPVNGEDKGDSGVDTQNSEGN
Retrocopy SGIQRDGPMKFEKDFDFKSANAQFNKEEIDREFHNKLKL<KKDKLEKQEKPVNGEDKGDSGVDTQNSEGN

Parental  ADEEDPLGPNCYYDKTKSFFDNISCDDNRERRPTWAEERRLNAETFGIPLRPNRGRGGYRGRGGLGFRGG
          ADEEDPLGPNCYYDKTKSF.DNISC.DNR..RPTWAEE.RLNAETFGIPLRPNR.RGGY.GRGGLGF.GG
Retrocopy ADEEDPLGPNCYYDKTKSFIDNISCNDNRKWRPTWAEE-RLNAETFGIPLRPNRDRGGYQGRGGLGFCGG

Parental  RGRGGGRGG
          RG..GGRGG
Retrocopy RGFRGGRGG

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	0.44 RPM	26.05 RPM
SRP051959_heart	0.30 RPM	36.73 RPM
SRP051959_kidney	0.42 RPM	42.15 RPM
SRP051959_liver	0.17 RPM	22.03 RPM
SRP051959_lung	0.33 RPM	42.98 RPM
SRP051959_lymph_node	0.09 RPM	47.05 RPM
SRP051959_skeletal_muscle	0.55 RPM	40.84 RPM
SRP051959_spleen	0.21 RPM	36.37 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3201 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3201 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3201 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006555	1 retrocopy	retro_chof_1375,
Callithrix jacchus	ENSCJAG00000010360	5 retrocopies	retro_cjac_1582, retro_cjac_2625, retro_cjac_3201 , retro_cjac_3327, retro_cjac_840,
Microcebus murinus	ENSMICG00000011598	1 retrocopy	retro_mmur_1605,
Myotis lucifugus	ENSMLUG00000003368	1 retrocopy	retro_mluc_1793,
Macaca mulatta	ENSMMUG00000021614	2 retrocopies	retro_mmul_1386, retro_mmul_1860,
Oryctolagus cuniculus	ENSOCUG00000011872	2 retrocopies	retro_ocun_193, retro_ocun_860,
Otolemur garnettii	ENSOGAG00000002492	2 retrocopies	retro_ogar_2586, retro_ogar_67,
Rattus norvegicus	ENSRNOG00000021133	1 retrocopy	retro_rnor_2397,
Ictidomys tridecemlineatus	ENSSTOG00000002785	1 retrocopy	retro_itri_170,