RetrogeneDB ID: retro_itri_514

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393297.1:16434364..16434994(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMB6
• Ensembl ID: ENSSTOG00000014871
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, beta type, 6 [Source:HGNC Symbol;Acc:9543]

Sequence

>retro_itri_514
TGGGAAAACCAGGAAGTCTCCACAGGGACCACTACCATGGCTGTGCAATTTGACTGGGGTGTGGTTCTGGGGGCGGACTC
CAGAACAACCATTGGGTCCTCTATCGCCAATCGAGTGATTGACAAGCTGACTCCTATTCATGACCACATTTTCAGCTGCC
GTAGAGGCTCTGTAGCTGACACCCAGGCTGTAGCAGATGCTGTCACTTATCAGCTTGGATTCCACAGCATTGAAATGAAT
GAGCCTCCATTGGTGCACACAGCAGCCAGTCTCTTTAAGGAGATGTGTTACCAATACTGGGAAGATCTGATGGCGGGAAT
TATCATTGCTGGCTGGGATCCTCAAGGAGGACAGGTATACTCAGTTCCCATGGGAGGTATGACGGTAAGGCAGTCCTTTG
CCATTGGAGGCTCTGGGAGTTCATATATCTATGGCAATGTTGATGCTACCTACCATGAAGGCATGACTAAGGAGGAGTGT
CTGCAGTTCACTGCCAATGCTCTTGCTTTGGCTATGGAACGGGACAGCTCCAGTGGAGGGGTGATCCGTCTGGCAGCCAT
TGAAGAATCGGGGGTAGAGCGGCAGATACTTTTGGGAGACCAGATACCCAAATTTACCATTGCTACTTTA

Alignment

ORF - retro_itri_514 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.47 %
• Parental protein coverage: 88.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  WENREVSTGTTIMAVQFDGGVVLGADSRTTTGSYIANRVTDKLTPIHDHIFCCRSGSAADTQAVADAVTY
          WEN.EVSTGTT.MAVQFD.GVVLGADSRTT.GS.IANRV.DKLTPIHDHIF.CR.GS.ADTQAVADAVTY
Retrocopy WENQEVSTGTTTMAVQFDWGVVLGADSRTTIGSSIANRVIDKLTPIHDHIFSCRRGSVADTQAVADAVTY

Parental  QLGFHSIELNEPPLVHTAASLFKEMCYRYREDLMAGIIIAGWDPQEGGQVYSVPMGGMMVRQSFAIGGSG
          QLGFHSIE.NEPPLVHTAASLFKEMCY.Y.EDLMAGIIIAGWDPQ.GGQVYSVPMGGM.VRQSFAIGGSG
Retrocopy QLGFHSIEMNEPPLVHTAASLFKEMCYQYWEDLMAGIIIAGWDPQ-GGQVYSVPMGGMTVRQSFAIGGSG

Parental  SSYIYGYVDATYREGMTKEECLQFTANALALAMERDGSSGGVIRLAAIEESGVERQVLLGDQIPKFTIAT
          SSYIYG.VDATY.EGMTKEECLQFTANALALAMERD.SSGGVIRLAAIEESGVERQ.LLGDQIPKFTIAT
Retrocopy SSYIYGNVDATYHEGMTKEECLQFTANALALAMERDSSSGGVIRLAAIEESGVERQILLGDQIPKFTIAT

Parental  L
          L
Retrocopy L

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_514 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_514 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000008036	2 retrocopies	retro_fcat_1813, retro_fcat_1995,
Loxodonta africana	ENSLAFG00000012859	1 retrocopy	retro_lafr_874,
Macropus eugenii	ENSMEUG00000010676	1 retrocopy	retro_meug_621,
Monodelphis domestica	ENSMODG00000005554	1 retrocopy	retro_mdom_799,
Rattus norvegicus	ENSRNOG00000019551	1 retrocopy	retro_rnor_56,
Sorex araneus	ENSSARG00000006615	1 retrocopy	retro_sara_689,
Ictidomys tridecemlineatus	ENSSTOG00000014871	1 retrocopy	retro_itri_514 ,