RetrogeneDB ID: retro_itri_767

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393319.1:3918086..3918546(-)
• Located in intron of: ENSSTOG00000015547

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARPC5L
• Ensembl ID: ENSSTOG00000007907
• Aliases: None
• Description: actin related protein 2/3 complex, subunit 5-like [Source:HGNC Symbol;Acc:23366]

Sequence

>retro_itri_767
ATAGCCCAGAACACGCTATCCTCGTGATTCCATCCAGTGGACATAAAAGAGTTGATGAGAACCAGTTGAGGAGCAAGAGG
AAGCCGTGGCTAGCAGGAAAGCCAGGCCCAGACCCTAAGCCCTAGCGAGGTGGATGGGCTTCTGTGGTAAGGGGGCCTGA
TTCGAGCCTTCCATGTAGCCTTGTAGAATTCAACAGTCAACACCAAAAATCAAGCTGTGAAGGAGCAAGCCCAAGGTGTG
GTGCTAAAAGTACTGACAAACTCGTAAGAGCAGTGAAGTTGAGCAGGCTGTATAGTCTCTGTACAGAAATGGCATTGACT
TTTTAATGAAGTATACTTATAAAGGGTTTGAGAAGCCCACAGAAATTAGCAGTGCAGCATTACTCCAATGGCACGGAAAG
GTCTTAGCTGTAGCGGGACTAGTCTCCATTATAAAAGTTCTTACAGCAGGAAAGACTGTT

Alignment

ORF - retro_itri_767 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.95 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MARNTLSSRFRRVDIDEF-DENKFVDEHEEAAAAAGEPGP-DPSEVDGLLRQWDMLRAFHAALRNSPVNT
          .A.NTLSS.F..VDI.E..DEN..........A....P.P..PSEVDGLL......RAFH.AL.NS.VNT
Retrocopy IAQNTLSS*FHPVDIKEL<DENQLRSKRKPWLAGKPGPDP>SPSEVDGLLW*GGLIRAFHVAL*NSTVNT

Parental  KNQAVKERAQGVVLKVLTNF-KSSEIEQAVQSLDRNGIDLLMKYIYKGFEKPTENSSAVLLQWHEKALAV
          KNQAVKE.AQGVVLKVLTN..KSSE.EQAV.SL.RNGID.LMKY.YKGFEKPTE.SSA.LLQWH.K.LAV
Retrocopy KNQAVKEQAQGVVLKVLTNS>KSSEVEQAV*SLYRNGIDFLMKYTYKGFEKPTEISSAALLQWHGKVLAV

Parental  GGLGSIIRVLTARKTV
          .GL.SII.VLTA.KTV
Retrocopy AGLVSIIKVLTAGKTV

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_767 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_767 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 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016540	1 retrocopy	retro_amel_1798,
Callithrix jacchus	ENSCJAG00000006730	4 retrocopies	retro_cjac_1282, retro_cjac_1725, retro_cjac_2744, retro_cjac_3941,
Felis catus	ENSFCAG00000028753	1 retrocopy	retro_fcat_1316,
Macaca mulatta	ENSMMUG00000020628	2 retrocopies	retro_mmul_1650, retro_mmul_623,
Mustela putorius furo	ENSMPUG00000013924	1 retrocopy	retro_mputfur_1532,
Oryctolagus cuniculus	ENSOCUG00000002997	1 retrocopy	retro_ocun_518,
Procavia capensis	ENSPCAG00000013936	1 retrocopy	retro_pcap_274,
Pan troglodytes	ENSPTRG00000021362	1 retrocopy	retro_ptro_2185,
Rattus norvegicus	ENSRNOG00000014317	1 retrocopy	retro_rnor_2730,
Ictidomys tridecemlineatus	ENSSTOG00000007907	2 retrocopies	retro_itri_275, retro_itri_767 ,
Tupaia belangeri	ENSTBEG00000008398	1 retrocopy	retro_tbel_442,