RetrogeneDB ID: retro_itri_1594

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393562.1:1703335..1704144(-)
• 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_1594
ATGGGTTTGTCAGCCTTTACTTCTGCTGTTCCAGTCAGACCTCACATGCTTCAGATCATCAGGTAGCATCACAACCTTCA
GGATGCCCAATGCATGAAAGGAAAATGAAAGGCTGTCCCATGTGAGCAGAACCCTCTGGTCCAACCTATGAGAGCAAAAC
ATGCTCTGTGCCTGCCCACCAAGAGGAGTATGTGCAGTGTTCCATTACAAGAACTGCTGCTAAGACTGACAGCCTGGATC
CTTCAAATCTGATCCTACCACCTAATCGAGCACCAGGGCCAGATCAGCCCTCTGGGTTGTCTACCATCATAGGGGAGTCA
TCCATTCGATAAGCAGGTTCAGAGAAAAAAGTGTTTTATCCTTCCAAACAGATGTTCTGTAATTCAATGTTAAGGAAAGG
GTGGAAGTGGAAAGACAGGATATTAGTGAGAAAGATATGTATAATATTAGAATTCACAGTCAGAACAATGAACAGGCTTG
GAAGGAGATTTTGAAGTGGGAAGCCCTTCATGCTGCCAATTGTCCTGTGGTTTATCATTGATCTCATTTGGAGGGAAAGC
AAAAGAATATTCACCAAGGGCAAGAATTGGTTCCTGGGTGGGGTGTGAGTTGCCTTTCGACAGGCATGATTGGATCATCA
ACCATGGTGGTACAGAAGTTAGACTGTGTGATAGATTACTACAGTGATGGCAAAGTCAGTGAGGACTACCTGTTCCCCAT
CCTGGACATCCACCTAGTCCCCCCACCTTTGGATTTACTTTCAGCTGTATCTGGACAGAATGGAGGTTGCTTGGTGGTGC
TAGACATCC

Alignment

ORF - retro_itri_1594 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.79 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MGLSASTPAVPV-QTSNASDHQTASPPSGCPMHEGKMKGCPMNAEPSGPTCESKAYSVPAHQDRAYEYVE
          MGLSA.T.AVPV.QTS.ASDHQ.AS.PSGCPMHE.KMKGCPM.AEPSGPT.ESK..SVPAHQ....EYV.
Retrocopy MGLSAFTSAVPV<QTSHASDHQVASQPSGCPMHERKMKGCPM*AEPSGPTYESKTCSVPAHQE---EYVQ

Parental  CPVTGGAAKNKENLDPSNLMPPPNQTPAPDQPFALSTVREESSIPRADSEKKWVYPSEQMFWNAMLRKGW
          C..T..AAK....LDPSNL..PPN..P.PDQP..LST...ESSI..A.SEKK..YPS.QMF.N.MLRKGW
Retrocopy CSITRTAAKT-DSLDPSNLILPPNRAPGPDQPSGLSTIIGESSIR*AGSEKKVFYPSKQMFCNSMLRKGW

Parental  KWKD-EDISQKDMYNIIKIHNQNNEQAWKEILKWEALHAAECP-CGPSLIRFGGKAKQYSPRARIRSWMG
          KWKD..DIS.KDMYN.I.IH.QNNEQAWKEILKWEALHAA.CP.CG.SLI.FGGKAK.YSPRARI.SW.G
Retrocopy KWKD<QDISEKDMYN-IRIHSQNNEQAWKEILKWEALHAANCP<CGLSLISFGGKAKEYSPRARIGSWVG

Parental  YELPFDRHDWIINRCGTEVRY-VIDYYDGGEVNKDYQFTILDVR---PALDSLSAV-WDRMKVAWWRWTS
          .ELPFDRHDWIIN..GTEVR..VIDYY..G.V..DY.F.ILD.....P.LD.LSAV..DRM.VAWW..TS
Retrocopy CELPFDRHDWIINHGGTEVRL>VIDYYSDGKVSEDYLFPILDIHLVPPPLDLLSAV>LDRMEVAWWC*TS

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_1594 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1594 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,