RetrogeneDB ID: retro_cjac_1582

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 17:9207552..9208378(-)
• Located in intron of: None

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_1582
ATGAGCGGGGGCACCCCTTGCATCGGAAGCAAGATCGGCCTCGTCTCTAAGGCGGAGATCCACTAGGAGGGCATCCTCTA
TACCATCAACACCGAAAACCCCACCGTAGCCCTCGCCAAAGTTCAATCCTTTGGTACAGAAGACAGACCAACAGATCGTC
TAATACCATCTCGAGATGAAGTCTTTGAATACATTATATTCCGTGAGAGTGACATTAAAGACCTCACTGTTTGTGAGCCA
CCAAAACCACAGTGTTCCTTGCCTCAAGACCCAGCTATCATTCAGTCCTCACTAGGCTCATCAACTTCTTCATTCCAGTC
CATGGGTTCTTATGGGCCTTTCAGCAGGATGCCCACACACAGTCAGTTCAGTCCAAGTTCCTTAGCTGGGCAGCAGTTTG
GTGCTGTTGGTATTGCTGGATGATCTTTGACATCCTTTGGAACAGAAACATCAAACAGTGGTACCTTACCCCAAAGTAGT
GCGGTTGGTTCTGCCTTTACACAGGATACAAGATCCCTAAAAACACAGTTATCTCAAGGTCGTTCAAGCCCTCAGTTAGA
CCCTTTGAGAAAAAGCCCAACCATGGAACAAGCAGTGCAGAGCGCCTTGGCCCACTTACCTGCTCCAGCACCTGTTGGGA
GGAGTCCTGTATCAACCAGGCCTTTGCCATCTACCAGCCAAAAAGCAACAGAGAATCAGGAGCACAGGCAAGCTGAAGTA
CACAAAGTTTCAAGGCCAGAAAATTAGCAACTCAGAAATGATAACAAGAAACAAGTAGCTCCAGGTGCTCCTTCAGCTCC
ATCGGGGTGGCAGGGGAAGATTTAGG

Alignment

ORF - retro_cjac_1582 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.53 %
• Parental protein coverage: 59.61 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSGGTPYIGSKISLISKAEIRYEGILYTIDTENSPVALAKVRSFGTEDRPTDRPIPPRDEVFEYIIFRGS
          MSGGTP.IGSKI.L.SKAEI..EGILYTI.TEN..VALAKV.SFGTEDRPTDR.IP.RDEVFEYIIFR.S
Retrocopy MSGGTPCIGSKIGLVSKAEIH*EGILYTINTENPTVALAKVQSFGTEDRPTDRLIPSRDEVFEYIIFRES

Parental  DIKDLTVCEPPKPQCSLPQDPAIVQSSLGSSTSSFQSMGSYGPFGRMPTYSQFSPSSLVGQQFGAVGVAG
          DIKDLTVCEPPKPQCSLPQDPAI.QSSLGSSTSSFQSMGSYGPF.RMPT.SQFSPSSL.GQQFGAVG.AG
Retrocopy DIKDLTVCEPPKPQCSLPQDPAIIQSSLGSSTSSFQSMGSYGPFSRMPTHSQFSPSSLAGQQFGAVGIAG

Parental  SSLTSFGTETSNSGTLPQSSAVGSAFTQDTRSLKTQLSQGRSSPQLDPLRKSPTMEQAVQTASAHLPAPA
          .SLTSFGTETSNSGTLPQSSAVGSAFTQDTRSLKTQLSQGRSSPQLDPLRKSPTMEQAVQ.A.AHLPAPA
Retrocopy *SLTSFGTETSNSGTLPQSSAVGSAFTQDTRSLKTQLSQGRSSPQLDPLRKSPTMEQAVQSALAHLPAPA

Parental  PVGRRSPVSTRPLPSTSQKAIENQEHRRAEVHKVSRPENEQLRNDNKRQVAPGAPSAP-RRGRGGHR
          PVG.RSPVSTRPLPSTSQKA.ENQEHR.AEVHKVSRPEN.QLRNDNK.QVAPGAPSAP.R.GRG..R
Retrocopy PVG-RSPVSTRPLPSTSQKATENQEHRQAEVHKVSRPEN*QLRNDNKKQVAPGAPSAP>RGGRGRFR

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

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1582 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1582 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1582 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,