RetrogeneDB ID: retro_itri_105

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393344.1:8580101..8581118(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000026905
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: FAM50A
• Ensembl ID: ENSSTOG00000004448
• Aliases: None
• Description: family with sequence similarity 50, member A [Source:HGNC Symbol;Acc:18786]

Sequence

>retro_itri_105
ATGGCGCAATACAAGGGCACCATGCGGGAGGCTGGCAGGGCCATGCACCTGATCAAGAAGCGGGAGAAGCAGAAGGAACA
GATGGAGGTGCTGAAGCAGCGCATCGCTGAAGAGACCATCATGAAGTCGAAGGTGGACAAAAAGTTCTCAGCTCACTACG
ATGCCGTGGAGGCCGAGCTCAAGTCCAGCACGGTGGGCCTGGTCACCCTGAACGACATGAAGGCCAAGCAGGAGGCCCTC
CTGAGGGAACGCGAGATGCAGCTGGCCAAGAAGGAACAGCTGGAAGAGCGCCGGCTGCAGCTGGAGTTGCTGCGCGAAAA
AGAGCGCAGGCTGGAGCGTAAGCGCAAGATCTCCAACCTGTCCTTCACGGTGGACGACGGCGACGGCGATGACCACTGCG
ATGACCGAGGCGACGATCGCAATGAAGGCGGCATGACCGAGGCCAGCAAGAGCAAGAAGAACCTGGGCAAGAATCCCGAC
GTGGACACGAGCTTCCTGCCAGATCGTGACCGTGAGGAGGAGGAGAACCGGCTCCGAGAGGAGCTGCGCAAGGAATGGGA
GGCCAAGCGCGAGAAGGTGAAGAGCGAGGAGATGGAGATCACCTTCAGCTACTGGGACGGCTCGGGGCACCGGCGCACCG
TGCGTATGAACAAGGGCAGCACCGTGCAGCAGTTCCTGAAAAAGGCGCTGCAGGGGCTGCGAAAGGACTTCCGCGAACTG
CGCTCGGCCGGCGTGGAGCAGCTCATGTACATCAAGGAGGACCTCATCCTGCCCCATTACCACACCTTCTACGATTTCAT
CATCGCCAAGGCCAGGGGCAAGAGCGGTCCGCTCTTCAACTTCGATGTGCACGATGACGTGAGGCTGCTCAGCGATGCCA
CCATGGAGAAGGACGAGTCACACGCAGGCAAAGTGGTGCTGCGGAGCTGGTATGAGAAGAACAAGCACATCTTCCCCGCC
AGCCGCTGGGAGCCCTACGATCCCGAGAAGAAGTGGGACAAGTACACCATCCGATGA

Alignment

ORF - retro_itri_105 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.35 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAQYKGAASEAGRAMHLMKKREKQREQMEQMKQRIAEENIMKSNIDKKFSAHYDAVEAELKSSTVGLVTL
          MAQYKG...EAGRAMHL.KKREKQ.EQME..KQRIAEE.IMKS..DKKFSAHYDAVEAELKSSTVGLVTL
Retrocopy MAQYKGTMREAGRAMHLIKKREKQKEQMEVLKQRIAEETIMKSKVDKKFSAHYDAVEAELKSSTVGLVTL

Parental  NDMKAKQEALVKEREKQLAKKEQSKELQLKLEKLREKERKKEAKRKISSLSFTLEEEEEGGEEEEEVAMY
          NDMKAKQEAL..ERE.QLAKKEQ..E..L.LE.LREKER..E.KRKIS.LSFT......G..........
Retrocopy NDMKAKQEALLREREMQLAKKEQLEERRLQLELLREKERRLERKRKISNLSFTVDDGD-GDDHCDDRGDD

Parental  EEELEREEITTKKRKLGKNPDVDTSFLPDRDREEEENRLREELRQEWEAKQEKIKSEEIEITFSYWDGSG
          ..E....E....K..LGKNPDVDTSFLPDRDREEEENRLREELR.EWEAK.EK.KSEE.EITFSYWDGSG
Retrocopy RNEGGMTEASKSKKNLGKNPDVDTSFLPDRDREEEENRLREELRKEWEAKREKVKSEEMEITFSYWDGSG

Parental  HRRTVKMKKGNTMQQFLQKALEILRKDFSELRSAGVEQLMYIKEDLIIPHHHSFYDFIVTKARGKSGPLF
          HRRTV.M.KG.T.QQFL.KAL..LRKDF.ELRSAGVEQLMYIKEDLI.PH.H.FYDFI..KARGKSGPLF
Retrocopy HRRTVRMNKGSTVQQFLKKALQGLRKDFRELRSAGVEQLMYIKEDLILPHYHTFYDFIIAKARGKSGPLF

Parental  NFDVHDDVRLLSDATVEKDESHAGKVVLRSWYEKNKHIFPASRWEPYDPEKKWDKYTVR
          NFDVHDDVRLLSDAT.EKDESHAGKVVLRSWYEKNKHIFPASRWEPYDPEKKWDKYT.R
Retrocopy NFDVHDDVRLLSDATMEKDESHAGKVVLRSWYEKNKHIFPASRWEPYDPEKKWDKYTIR

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_105 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_105 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 12 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000273	1 retrocopy	retro_amel_15,
Felis catus	ENSFCAG00000011399	1 retrocopy	retro_fcat_100,
Homo sapiens	ENSG00000071859	1 retrocopy	retro_hsap_94,
Loxodonta africana	ENSLAFG00000008766	1 retrocopy	retro_lafr_43,
Myotis lucifugus	ENSMLUG00000022234	1 retrocopy	retro_mluc_7,
Mustela putorius furo	ENSMPUG00000009476	1 retrocopy	retro_mputfur_145,
Mus musculus	ENSMUSG00000001962	1 retrocopy	retro_mmus_103,
Nomascus leucogenys	ENSNLEG00000014266	1 retrocopy	retro_nleu_109,
Rattus norvegicus	ENSRNOG00000045790	1 retrocopy	retro_rnor_214,
Sorex araneus	ENSSARG00000006465	1 retrocopy	retro_sara_554,
Sus scrofa	ENSSSCG00000025303	1 retrocopy	retro_sscr_56,
Ictidomys tridecemlineatus	ENSSTOG00000004448	10 retrocopies	retro_itri_105 , retro_itri_1563, retro_itri_1688, retro_itri_1691, retro_itri_1693, retro_itri_1758, retro_itri_1760, retro_itri_1762, retro_itri_1780, retro_itri_184,