RetrogeneDB ID: retro_mmus_3285

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 9:63898263..63898802(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Arl1
• Ensembl ID: ENSMUSG00000060904
• Aliases: Arl1, 2310008D22Rik, AU019749
• Description: ADP-ribosylation factor-like 1 [Source:MGI Symbol;Acc:MGI:99436]

Sequence

>retro_mmus_3285
ATGGGTGGCTTTTTCTCAAGTATTTTTTCCAGTCTCTTTGGAACCAGAGAAATGAGGATTTTAATTTTGGGATTAGATGG
TGCTGGAAAAACAACAATTTTGTACAGGTTACAGGTTGGAGAAGTTATTACTACTATTCCCACTATTGGATTTAATGTGG
AGACGGTGACATACAAAAATCTCAAATTCCAATTTGGGACTTAGGAGGACAGACAAGTATCAGGCCATACTGGAGATGTT
ATTATTCAAAAACAGATGCAGTCATCTATGTCGTTGACAGTTGTGACTGAGACCGAATTGGCATTTCCAAGTCTGAGTTA
GTTGCCATGTTGGAGGAAGAAGAGCTGAGAAAAGCCATTTTAGTGATGTTTGCAAATAAGCAGGACATGGAACAGGCCAT
GACACCCTCAGAAATGGCAAATGCTCTTGGGTTACCTGCCCTGAAGGACCGGAAGTGGCAGATCTTTAAAACTTCAGCAA
CCAAAGGCACTGGCCTTGATGAGGCAATGGAATGGTTAGTTGAAACCCTGAAAAGCAGA

Alignment

ORF - retro_mmus_3285 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.69 %
• Parental protein coverage: 99.45 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGGFFSSIFSSLFGTREMRILILGLDGAGKTTILYRLQVGEVVTTIPTIGFNVETVTYKNLKFQ-VWDLG
          MGGFFSSIFSSLFGTREMRILILGLDGAGKTTILYRLQVGEV.TTIPTIGFNVETVTYKNLKFQ..WDLG
Retrocopy MGGFFSSIFSSLFGTREMRILILGLDGAGKTTILYRLQVGEVITTIPTIGFNVETVTYKNLKFQ<IWDLG

Parental  GQTSIRPYWRCYYSNTDAVIYVVDSCDRDRIGISKSELVAMLEEEELRKAILVVFANKQDMEQAMTPSEM
          GQTSIRPYWRCYYS.TDAVIYVVDSCD.DRIGISKSELVAMLEEEELRKAILV.FANKQDMEQAMTPSEM
Retrocopy GQTSIRPYWRCYYSKTDAVIYVVDSCD*DRIGISKSELVAMLEEEELRKAILVMFANKQDMEQAMTPSEM

Parental  ANALGLPALKDRKWQIFKTSATKGTGLDEAMEWLVETLKSR
          ANALGLPALKDRKWQIFKTSATKGTGLDEAMEWLVETLKSR
Retrocopy ANALGLPALKDRKWQIFKTSATKGTGLDEAMEWLVETLKSR

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
SRP007412_brain	0.19 RPM	55.39 RPM
SRP007412_cerebellum	0.13 RPM	44.81 RPM
SRP007412_heart	0.16 RPM	44.70 RPM
SRP007412_kidney	0.19 RPM	54.75 RPM
SRP007412_liver	0.08 RPM	61.66 RPM
SRP007412_testis	0.09 RPM	50.77 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3285 was not detected

EST

No EST(s) were mapped for retro_mmus_3285 retrocopy.

TSS

No TSS is located nearby retro_mmus_3285 retrocopy 5' end.

Lab

retro_mmus_3285 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3285 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 19 parental genes, and 35 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,
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	ENSMUSG00000036093	1 retrocopy	retro_mmus_2232,
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,