RetrogeneDB ID: retro_cjac_2625

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:76930746..76931635(-)
• 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_2625
ATGAGCGGGGGCACCCCTTACATCGGCAGCAAGATAAGCCTCATCTCCAAGGCAGAGATCCTCTACGAGGGCATCCTCTA
CACCATGGACACCGAAAACTCCACTGTAGCCCTCGCCAAAGTTCCATCCTTTGGTACAGAAGACAGACCAACAGATCGTC
CAATACCACCTCGAGATGAAGTCTTTGAATATATTATATTCCGTGGGAGTGACATTAAAGACCTCACTGTTTGTGAGCCA
CCAAAACCACAGTGTTCTTTGCCTCAAGACCCAGCTATCGTTCGGTCCTCACTAGGCTCATTGACTTCTTCATTCCAGTC
CATGGGTTCTTATGGGCCTTTCGGCAGGATGCCCACATACAGTCAGTTCAGTCCAGGTTCCTTAGTTGGGCAGCAGTTTG
GTGCTGTTCGTGTTGCTGGAAGCTCTTTCACATCCTTTGGAACAGAGACATCAAACAGTGGTACCTTACCCCAAAGTAGT
GCGGTTGGTTCTTCCTTTACACAGGATACAGGAGCCCTAAAAACACAGTTATCTCAAGGTCGTTCAAGCCCTCAGTTAGA
CCCTTTGAGAAAAAGCCCAACCATGGAACAAGCAGTGGAGACTGCCTCGGCCCACTTACCTGCTCCAGCACCTGTTGGGA
GAAGGAGCCCTGTTATCAACCAGGCCTTTGCCATCTACCAGCCAAAAAGCAATAGAGAATCAGGGGCACAGGAGAGCTGA
AGTACACAAAGTTTCAAGGCCAGAAAATGAGCAACTCAGAAATGATAACAAGAGACAAGTAGCTCCAGGTGCTCCTTCAG
CTCCAAGGAGAGGGCGTGGGGGTCATCGGGGTGGCAGGGGAAGATTTGGTATTCGGCGAGATGGGCCAATGAAATTTGAG
AAAGACTTT

Alignment

ORF - retro_cjac_2625 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.95 %
• Parental protein coverage: 63.93 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSGGTPYIGSKISLISKAEIRYEGILYTIDTENSPVALAKVRSFGTEDRPTDRPIPPRDEVFEYIIFRGS
          MSGGTPYIGSKISLISKAEI.YEGILYT.DTENS.VALAKV.SFGTEDRPTDRPIPPRDEVFEYIIFRGS
Retrocopy MSGGTPYIGSKISLISKAEILYEGILYTMDTENSTVALAKVPSFGTEDRPTDRPIPPRDEVFEYIIFRGS

Parental  DIKDLTVCEPPKPQCSLPQDPAIVQSSLGSSTSSFQSMGSYGPFGRMPTYSQFSPSSLVGQQFGAVGVAG
          DIKDLTVCEPPKPQCSLPQDPAIV.SSLGS.TSSFQSMGSYGPFGRMPTYSQFSP.SLVGQQFGAV.VAG
Retrocopy DIKDLTVCEPPKPQCSLPQDPAIVRSSLGSLTSSFQSMGSYGPFGRMPTYSQFSPGSLVGQQFGAVRVAG

Parental  SSLTSFGTETSNSGTLPQSSAVGSAFTQDTRSLKTQLSQGRSSPQLDPLRKSPTMEQAVQTASAHLPAPA
          SS.TSFGTETSNSGTLPQSSAVGS.FTQDT..LKTQLSQGRSSPQLDPLRKSPTMEQAV.TASAHLPAPA
Retrocopy SSFTSFGTETSNSGTLPQSSAVGSSFTQDTGALKTQLSQGRSSPQLDPLRKSPTMEQAVETASAHLPAPA

Parental  PVGRRSPV-STRPLPSTSQKAIENQEHRRAEVHKVSRPENEQLRNDNKRQVAPGAPSAPRRGRGGHRGGR
          PVGRRSPV.STRPLPSTSQKAIENQ.HRRAEVHKVSRPENEQLRNDNKRQVAPGAPSAPRRGRGGHRGGR
Retrocopy PVGRRSPV>STRPLPSTSQKAIENQGHRRAEVHKVSRPENEQLRNDNKRQVAPGAPSAPRRGRGGHRGGR

Parental  GRFGIRRDGPMKFEKDF
          GRFGIRRDGPMKFEKDF
Retrocopy GRFGIRRDGPMKFEKDF

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	1.93 RPM	26.05 RPM
SRP051959_heart	2.12 RPM	36.73 RPM
SRP051959_kidney	3.22 RPM	42.15 RPM
SRP051959_liver	1.52 RPM	22.03 RPM
SRP051959_lung	2.94 RPM	42.98 RPM
SRP051959_lymph_node	2.88 RPM	47.05 RPM
SRP051959_skeletal_muscle	2.31 RPM	40.84 RPM
SRP051959_spleen	2.06 RPM	36.37 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2625 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2625 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2625 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,