RetrogeneDB ID: retro_cjac_2938

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:120385750..120386284(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000007397
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ARL1
• Ensembl ID: ENSCJAG00000001966
• Aliases: None
• Description: ADP-ribosylation factor-like 1 [Source:HGNC Symbol;Acc:692]

Sequence

>retro_cjac_2938
ATGGGTGGTTTTTTCTCAAGTATATCTTCCAGTCTGTTTGGAGCTCAGGAAATGAAGATTTTAATTTTGGGATTAGACGG
AGCAGCAAAAACCAAAATTTTGTACAGATTACAAATTGGAGAAGTCTTTACTGCTATACCTACCATCGGATATAATGTAG
AGATGGTGACATACAAAAACTTTAAATTCCAACTCTGGGATTTAGGAGGACAGACAAGTATCAGGCCATACTGGAGATGT
TACTATTCAAACACAGATGCAGTCATTTATGTAGTAGACTGTTGTGACCAAGACCGAATTGGCATTTCCAAATCAGAGTT
AGTTGCCATGTTGGAGGAAGAAGAGCTGAGAAAAGCCATTTTAGTGGTGTTTGCAGGACATGGAACAGGCCATGACTTCC
TCAGAGATGGCAAATTTACTTTGGCTACCTGTCTTGAAGGACTGAAAATGGCAATATTCAAAACATCAGCAACCAAAGGC
ACTAGCCTTGATGAGGCAATGGAATGGTTAGTTGAAACGTTGAAAAGCAGACAG

Alignment

ORF - retro_cjac_2938 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.38 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGGFFSSIFSSLFGTREMRILILGLDGAGKTTILYRLQVGEVVTTIPTIGFNVETVTYKNLKFQVWDLGG
          MGGFFSSI.SSLFG..EM.ILILGLDGA.KT.ILYRLQ.GEV.T.IPTIG.NVE.VTYKN.KFQ.WDLGG
Retrocopy MGGFFSSISSSLFGAQEMKILILGLDGAAKTKILYRLQIGEVFTAIPTIGYNVEMVTYKNFKFQLWDLGG

Parental  QTSIRPYWRCYYSNTDAVIYVVDSCDRDRIGISKSELVAMLEEEELRKAILVVFANKQDMEQAMTPSEMA
          QTSIRPYWRCYYSNTDAVIYVVD.CD.DRIGISKSELVAMLEEEELRKAILVVFA...............
Retrocopy QTSIRPYWRCYYSNTDAVIYVVDCCDQDRIGISKSELVAMLEEEELRKAILVVFAGHGTGHDFLRDGKFT

Parental  NSLGLPALKDRKWQIFKTSATKGTGLDEAMEWLVETLKSRQ
          ....L..LK........T..T....LDEAMEWLVETLKSRQ
Retrocopy LATCLEGLKMAIFKTSATKGT---SLDEAMEWLVETLKSRQ

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	38.05 RPM
SRP051959_heart	0.00 RPM	41.41 RPM
SRP051959_kidney	0.00 RPM	51.29 RPM
SRP051959_liver	0.13 RPM	36.15 RPM
SRP051959_lung	0.00 RPM	35.93 RPM
SRP051959_lymph_node	0.00 RPM	29.11 RPM
SRP051959_skeletal_muscle	0.00 RPM	42.89 RPM
SRP051959_spleen	0.04 RPM	41.18 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2938 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2938 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2938 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016452	2 retrocopies	retro_amel_1138, retro_amel_713,
Canis familiaris	ENSCAFG00000006992	2 retrocopies	retro_cfam_1176, retro_cfam_709,
Callithrix jacchus	ENSCJAG00000001966	1 retrocopy	retro_cjac_2938 ,
Callithrix jacchus	ENSCJAG00000003311	9 retrocopies	retro_cjac_1054, retro_cjac_1111, retro_cjac_1255, retro_cjac_1921, retro_cjac_2949, retro_cjac_3920, retro_cjac_4131, retro_cjac_4175, retro_cjac_4211,
Echinops telfairi	ENSETEG00000020310	1 retrocopy	retro_etel_1850,
Macropus eugenii	ENSMEUG00000015525	1 retrocopy	retro_meug_518,
Myotis lucifugus	ENSMLUG00000002351	1 retrocopy	retro_mluc_255,
Monodelphis domestica	ENSMODG00000003056	1 retrocopy	retro_mdom_677,
Mustela putorius furo	ENSMPUG00000011822	1 retrocopy	retro_mputfur_1458,
Mus musculus	ENSMUSG00000060904	1 retrocopy	retro_mmus_3285,
Oryctolagus cuniculus	ENSOCUG00000002217	5 retrocopies	retro_ocun_1608, retro_ocun_399, retro_ocun_400, retro_ocun_465, retro_ocun_847,
Otolemur garnettii	ENSOGAG00000015144	1 retrocopy	retro_ogar_1239,
Pteropus vampyrus	ENSPVAG00000008119	2 retrocopies	retro_pvam_1072, retro_pvam_715,
Rattus norvegicus	ENSRNOG00000005763	1 retrocopy	retro_rnor_2375,
Sorex araneus	ENSSARG00000013944	4 retrocopies	retro_sara_237, retro_sara_304, retro_sara_479, retro_sara_71,
Sarcophilus harrisii	ENSSHAG00000004634	2 retrocopies	retro_shar_204, retro_shar_275,
Ictidomys tridecemlineatus	ENSSTOG00000016022	2 retrocopies	retro_itri_1000, retro_itri_348,
Tarsius syrichta	ENSTSYG00000013257	5 retrocopies	retro_tsyr_1803, retro_tsyr_188, retro_tsyr_350, retro_tsyr_369, retro_tsyr_809,
Tursiops truncatus	ENSTTRG00000017202	1 retrocopy	retro_ttru_701,