RetrogeneDB ID: retro_itri_1000

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393357.1:3073376..3073920(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000027221
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ARL1
• Ensembl ID: ENSSTOG00000016022
• Aliases: None
• Description: ADP-ribosylation factor-like 1 [Source:HGNC Symbol;Acc:692]

Sequence

>retro_itri_1000
ATGGGTGGCTTTTTCTCAAGTATTTTTTTCCAGTCTCTTTGGAACCCGGGAAATGAGGATTTTAATTTTGGGATTAGATG
GTGCAGGAAAAACCACAATTCTGTACAGATTACAAGTTGGAGAAGTTGTTACTACTATTCCTACTATTGGATTTAATGTA
GAGACGGTGACATACAAAAACCTTAAATTCCAAGTTTGGGATTTAGGAGGACAGACAAGTATCAGGCCATACTGGAGATG
TTATTATTCAAACACCGATGCAGTCATTTATGTAGTAGACAGTTGTGACCGAGACCGAATTGGCATTTCTAAATCAGAGT
TAGTTGCCATGTTGGAGGAAGAAGAGCTGAGAAAAGCCATTTTAGTGGTGTTTGCAAATAAACAAGACATGGAGCAGGCT
ATGACTCCCTCAGAGATGGCAAACTCACTTGGATTACCTGCCTTGAAGGACCAAAAATGGCAGATATTCAAAACATCAGC
AACCAAAGGCACTGGCCTTGATGAAGCAATGGAATGGTTAGTTGAAACATTAAAAAGCAGACAG

Alignment

ORF - retro_itri_1000 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.9 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGGFFSSI-FSSLFGTREMRILILGLDGAGKTTILYRLQVGEVVTTIPTIGFNVETVTYKNLKFQVWDLG
          MGGFFSSI.FSSLFGTREMRILILGLDGAGKTTILYRLQVGEVVTTIPTIGFNVETVTYKNLKFQVWDLG
Retrocopy MGGFFSSI>FSSLFGTREMRILILGLDGAGKTTILYRLQVGEVVTTIPTIGFNVETVTYKNLKFQVWDLG

Parental  GQTSIRPYWRCYYSNTDAVIYVVDSCDRDRIGISKSELVAMLEEEELRKAILVVFANKQDMEQAMTPSEM
          GQTSIRPYWRCYYSNTDAVIYVVDSCDRDRIGISKSELVAMLEEEELRKAILVVFANKQDMEQAMTPSEM
Retrocopy GQTSIRPYWRCYYSNTDAVIYVVDSCDRDRIGISKSELVAMLEEEELRKAILVVFANKQDMEQAMTPSEM

Parental  ANSLGLPALKDRKWQIFKTSATKGTGLDEAMEWLVETLKSRQ
          ANSLGLPALKD.KWQIFKTSATKGTGLDEAMEWLVETLKSRQ
Retrocopy ANSLGLPALKDQKWQIFKTSATKGTGLDEAMEWLVETLKSRQ

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_1000 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1000 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 37 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	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	ENSSTOG00000011104	1 retrocopy	retro_itri_1390,
Ictidomys tridecemlineatus	ENSSTOG00000016022	2 retrocopies	retro_itri_1000 , retro_itri_348,
Ictidomys tridecemlineatus	ENSSTOG00000016326	1 retrocopy	retro_itri_62,
Ictidomys tridecemlineatus	ENSSTOG00000027859	1 retrocopy	retro_itri_580,
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,