RetrogeneDB ID: retro_itri_1563

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393541.1:76117..77024(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000026658
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_1563
GAGGAGAACATAATGAAATCCAACATTGACAAGAAGTTCTCTGCACACTAGGATGCTGTGAAGGCAGAGCTCAAGTCCAG
CACCGTCGGCCTTGTGACCCTGAATGACATGAAAGCCTAACAGGAAGCACTGGTGAAGGAGCAGGAGAAGCAGCTGGCCA
AGAGGGAGCACTCAAAGGAGCTGCAGCTAAAGCTGGAGAAGCTGCGAGAAAAGAGCACCAGAAGGAGGCCAAGCAGAAGA
TCTCTAGCCTGTCCTTCACCTTGGAGGAAGAAGAGGAGGGAGACAAAGAGGAGGAGGAGGTGGCCATGCATGAGGAGGAG
CTGGAAAGGGAAGAGATCACCACAAAGAGAAGGAAATTGGGGAAGAACCCAGATGTGGACACCAGTTTCTTGCCTGACCA
AGACAGGGAGGAGGCGGAAAATCGTCTCCAGGAAGAGCTGCAGCAGGAGTGGGAAGCCAAGCAGGAGAAGGTTAAGAGTG
AAGAGATTGAAATCACCTTCAGTTACTGGGCTGGCTCTGGACACCAGCCGACAGTCAAAATGGAAAAGGGCAATACAATG
CAGCCGTTCCTCCAGAAGGCACTTGAGATCCTGCGTGAAGACTTCAGTAAGGTCAGGTCAGCAGGGGTGGGGCAGCTCAT
GTACATCAAGGAGGACTAATCATTCCCCACCATCACAGTTTCTGTGACTTCATCGTTACCAAGGCACGTGGGAAGAATTG
GCCACTCTGTAACTTTGATCTTCATGATAATGGGCGGCTACTCAGCGATGCCACTGTGGAGAAGTATGAGTCTCATTCAG
GAAAAGTGGTGCTGAGGAGCTGGTATGAGAAGAACAAGCACATCTTCCCTGCCATCTGCTGGGAGCCCTATGACCCTGAA
AAGAAGTGGGACAAGTATAAGATCCGG

Alignment

ORF - retro_itri_1563 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.3 %
• Parental protein coverage: 89.38 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EENIMKSNIDKKFSAHYDAVEAELKSSTVGLVTLNDMKAKQEALVKEREKQLAKKEQSKELQLKLEKLRE
          EENIMKSNIDKKFSAH.DAV.AELKSSTVGLVTLNDMKA.QEALVKE.EKQLAK.E.SKELQLKLEKLRE
Retrocopy EENIMKSNIDKKFSAH*DAVKAELKSSTVGLVTLNDMKA*QEALVKEQEKQLAKREHSKELQLKLEKLRE

Parental  K-ERKKEAKRKISSLSFTLEEEEEGGEEEEEVAMYEEELEREEITTKKRKLGKNPDVDTSFLPDRDREEE
          K.E..KEAK.KISSLSFT..............AM.EEELEREEITTK.RKLGKNPDVDTSFLPD.DREE.
Retrocopy K<EHQKEAKQKISSLSFTXXXXXXXXXXXXXXAMHEEELEREEITTKRRKLGKNPDVDTSFLPDQDREEA

Parental  ENRLREELRQEWEAKQEKIKSEEIEITFSYWDGSGHRRTVKMKKGNTMQQFLQKALEILRKDFSELRSAG
          ENRL.EEL.QEWEAKQEK.KSEEIEITFSYW.GSGH..TVKM.KGNTMQ.FLQKALEILR.DFS..RSAG
Retrocopy ENRLQEELQQEWEAKQEKVKSEEIEITFSYWAGSGHQPTVKMEKGNTMQPFLQKALEILREDFSKVRSAG

Parental  VEQLMYIKED-LIIPHHHSFYDFIVTKARGKSGPLFNFDVHDDVRLLSDATVEKDESHAGKVVLRSWYEK
          V.QLMYIKED.LIIPHHHSF.DFIVTKARGK..PL.NFD.HD..RLLSDATVEK.ESH.GKVVLRSWYEK
Retrocopy VGQLMYIKED<LIIPHHHSFCDFIVTKARGKNWPLCNFDLHDNGRLLSDATVEKYESHSGKVVLRSWYEK

Parental  NKHIFPASRWEPYDPEKKWDKYTVR
          NKHIFPA..WEPYDPEKKWDKY..R
Retrocopy NKHIFPAICWEPYDPEKKWDKYKIR

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_1563 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1563 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,