RetrogeneDB ID: retro_cjac_3327

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:94240259..94241192(-)
• Located in intron of: ENSCJAG00000014635

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_3327
ATATTCCATGGAAGTGACATTAGAGACCTCACTGTGAACCACCAAAACCAGTGTTCTTTGCCTCAAGACCCAGCTATCAT
TCATTCCTCTCTAGGCTCATCAACTTTTTCATTCCAGTCCATGGGTTCTTATGGGCCTTTTAGCAGGATGCTCACATACA
GTCAGGTTAGTCCAAGTTCCTTGGTTGGGAAGCACTTTGGTGCTGCTGGTAATGCTAGAAGCTCTTTGACGTTCTTTGGA
ACAGAAACATCAAACAGTGATAACTCACCCCAAAGTAGGGTGTTGGGTTTTGCTTTTACACAGGATATAAGATCTCTAAA
AAATGCAGTTATGTTAAGGTCATTCAAGCCCTCAGTTAGACTCTTTGGGAAAAGCCCAACCACGTAACCAGCAGTGCAGA
CCACCTTGGCCCATTTACCTGCTCCAGCACTTGTTGGGAGAAGGAGTCCTGTATCAGCCAGGCCTTTGCCATCTACCAGC
TAAAAAGCAATAGAGAATCAAGACCACAGGTGAGCTGAAGTACACAAAGTTTCAAAGCCAGAAAATGAGCAACTATGAAA
TGATAGCAAGAGACAAGTAGCTCCAGGGGCTCCTTCAGCACCAAGGAGAGGACATGCAGGTCATTAGGGTGGTAGAGGAA
GATCTCGTATTCCGCGAGATGGGCCAACAAAATTTGAGAAAGACTTTGAAAGTACAAATGCACAATTCAACAAGGAAGAG
ACTGACAGAGAGTTTCATAATAAACTTAGAAGAAGATAAATTGAGAAACAGGAGAAGCCTGTAAATGGTGAAGATAAAGG
CGACTCAGGAGTTGATACCCAAAACAGTGAAAGAAATGCTGATAAAGAAGATCCACTTGGACCTAACTGCTATTATGACA
AAACGAAATCCTTCTTTGATAATATTTCTTGTGATGACAATAGTGAACGGAGA

Alignment

ORF - retro_cjac_3327 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.06 %
• Parental protein coverage: 68.47 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IFRGSDIKDLTVCEPPKPQCSLPQDPAIVQSSLGSSTSSFQSMGSYGPFGRMPTYSQFSPSSLVGQQFGA
          IF.GSDI.DLTV......QCSLPQDPAI..SSLGSST.SFQSMGSYGPF.RM.TYSQ.SPSSLVG..FGA
Retrocopy IFHGSDIRDLTVNH--QNQCSLPQDPAIIHSSLGSSTFSFQSMGSYGPFSRMLTYSQVSPSSLVGKHFGA

Parental  VGVAGSSLTSFGTETSNSGTLPQSSAVGSAFTQDTRSLKT-QLSQGRSSPQLDPLRK-SPTMEQAVQTAS
          .G.A.SSLT.FGTETSNS...PQS...G.AFTQD.RSLK..QL..G.SSPQLD.L.K.SPT...AVQT..
Retrocopy AGNARSSLTFFGTETSNSDNSPQSRVLGFAFTQDIRSLKN>QLC*GHSSPQLDSLGK<SPTT*PAVQTTL

Parental  AHLPAPAPVGRRSPVSTRPLPSTSQKAIENQEHRRAEVHKVSRPENEQLRNDNKRQVAPGAPSAPRRGRG
          AHLPAPA.VGRRSPVS.RPLPSTS.KAIENQ.HR.AEVHKVS.PENEQL.ND.KRQVAPGAPSAPRRG..
Retrocopy AHLPAPALVGRRSPVSARPLPSTS*KAIENQDHR*AEVHKVSKPENEQL*NDSKRQVAPGAPSAPRRGHA

Parental  GHRGGRGRFGIRRDGPMKFEKDFDFESANAQFNKEEIDREFHNKLKLKEDKLEKQEKPVNGEDKGDSGVD
          GH.GGRGR..I.RDGP.KFEK..DFES.NAQFNKEE.DREFHNKL.......EKQEKPVNGEDKGDSGVD
Retrocopy GH*GGRGRSRIPRDGPTKFEK--DFESTNAQFNKEETDREFHNKLRRR--*IEKQEKPVNGEDKGDSGVD

Parental  TQNSEGNADEEDPLGPNCYYDKTKSFFDNISCDDNRERR
          TQNSE.NAD.EDPLGPNCYYDKTKSFFDNISCDDN.ERR
Retrocopy TQNSERNADKEDPLGPNCYYDKTKSFFDNISCDDNSERR

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	26.05 RPM
SRP051959_heart	0.09 RPM	36.73 RPM
SRP051959_kidney	0.04 RPM	42.15 RPM
SRP051959_liver	0.09 RPM	22.03 RPM
SRP051959_lung	0.05 RPM	42.98 RPM
SRP051959_lymph_node	0.00 RPM	47.05 RPM
SRP051959_skeletal_muscle	0.00 RPM	40.84 RPM
SRP051959_spleen	0.02 RPM	36.37 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3327 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3327 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3327 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,