RetrogeneDB ID: retro_itri_1277

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393423.1:5008940..5009455(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HCCS
• Ensembl ID: ENSSTOG00000014037
• Aliases: None
• Description: holocytochrome c synthase [Source:HGNC Symbol;Acc:4837]

Sequence

>retro_itri_1277
TTGGGTTTGTCACCCTCTACTCCTACTGTTCCTGTTCAGACCTCAAATGATTCAGATCTTCAGACAGCATCCTCAAATTC
AGGATGGCTGATACGTGAAGGGAAAATGAAAGGCTGTAGGAAGAGCACAGAACCCTCTGGTCCAGGCTCTGAGAGCAAAA
CATACTCTGCCTGCCCTCCAAGATCCTGCATATGAGTACGTACAGTGTGTCCCATTGCCAGCTCTGCTGCTAAGAATAAG
GAGAACATGAATCCTTCAAATCTGATGCCACCACCTAACCAAACACCGGCTCCAGATCAGCCCTTTGCATTGTCTACCGC
CAGAGAGGAGTCATCCACTCCACGAGCAGATTTAGAGAAAACACGGGTTTATCCTTCCTAACTGATGCTCTGGAATGAAA
AGTTTAGGAAAGGGTGGAAGTGGAAGGATGAGGATACTAATCAGAAAAATATGTGTAATACCATCAGAATTCACAGTCAA
ACAATTCACAGGCGTGGAGAGAGATTTTGAAGTAT

Alignment

ORF - retro_itri_1277 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.9 %
• Parental protein coverage: 63.24 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGLSASTPAVPVQTSNASDHQTASPPSGCPMHEGKMKGCPMNAEPSGPTCESKAYSVPAHQDRAYEYVEC
          .GLS.STP.VPVQTSN.SD.QTAS..SG....EGKMKGC....EPSGP..ESK.YS.............C
Retrocopy LGLSPSTPTVPVQTSNDSDLQTASSNSGWLIREGKMKGCRKSTEPSGPGSESKTYSACPPRSCI*VRTVC

Parental  PVTGGAAKNKENLDPSNLMPPPNQTPAPDQPFALSTVREESSIPRADSEKKWVYPSEQMFWNAMLRKGWK
          P....AAKNKEN..PSNLMPPPNQTPAPDQPFALST.REESS.PRAD.EK..VYPS..M.WN...RKGWK
Retrocopy PIASSAAKNKENMNPSNLMPPPNQTPAPDQPFALSTAREESSTPRADLEKTRVYPS*LMLWNEKFRKGWK

Parental  WKDEDISQKDMYNIIKIHNQ-NNEQAWKEILKW
          WKDED..QK.M.N.I.IH.Q.NN.QAW.EILK.
Retrocopy WKDEDTNQKNMCNTIRIHSQ<NNSQAWREILKY

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_1277 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1277 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 4 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000022393	1 retrocopy	retro_fcat_1706,
Myotis lucifugus	ENSMLUG00000003569	1 retrocopy	retro_mluc_1621,
Ictidomys tridecemlineatus	ENSSTOG00000014037	6 retrocopies	retro_itri_1277 , retro_itri_1462, retro_itri_1594, retro_itri_1700, retro_itri_242, retro_itri_745,
Tupaia belangeri	ENSTBEG00000002670	1 retrocopy	retro_tbel_1503,