RetrogeneDB ID: retro_itri_1805

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393843.1:277027..277658(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS7
• Ensembl ID: ENSSTOG00000015200
• Aliases: None
• Description: mitochondrial ribosomal protein S7 [Source:HGNC Symbol;Acc:14499]

Sequence

>retro_itri_1805
CAGGTTAGGTGGGACAGCTATGGTTCCAAATCCAGGAATTCCCAAGTTGACAAAGAATGTTACCTCAAGCCTGAAGTTGA
GCTCACCTAGGAGGACAAATGTGACAAGGGTCATAAGACAACTGAACTCATCAAAGCTACAAAAGAAACAAAAGCAAGTT
CAATGTTTGCAAATCCAAAGATCCGTATATTTGTTGACATGATGAGGAAAGGAGGAAACAAATTACTACCAGATTCCTCA
GGATGCAGACTGAAAGGTGTTAAAAGGAAGTGGTTTGAGAAATAACATGCTGCTATTCCAGAGGAACAAGCAACCATTCA
AAGCAACCCCTACATCATCTTCCACCAAGCACTGTATAACTGAGCTCTGATTGGAATGGTACCTATTCAATACAAGTGTG
GTCATTTCTACCAGGTCCCTGGACCTCCAGCTGACCGATGTAGCCACTTCCTGGCCATGAAATAAATTATCACTGAATGC
CAAAAGACTAATCATGAGTGGACACTAACGCCAGAGAGCCTGTCACATAAACTGCTGCAGGCTTTCACAACTACAGTCCT
ATGATCCAGACAAAGCATGACAGGTACACAATAGCAGAGGCCAACTGTGCCCTGGTCACTATTTGTGGTGG

Alignment

ORF - retro_itri_1805 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.21 %
• Parental protein coverage: 87.6 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QVRWSRYGAEFRDPLIDKEHYRKSMAELTEEEKYDQELKKTQLIKAAPATKTSSVFADPVISKFTNMMMK
          QVRW..YG...R....DKE.Y.K...ELT.E.K.D...K.T.LIKA...TK.SS.FA.P.I..F..MM.K
Retrocopy QVRWDSYGSKSRNSQVDKECYLKPEVELT*EDKCDKGHKTTELIKATKETKASSMFANPKIRIFVDMMRK

Parental  GGNKVLARSLMNQTLESVKRKQFEKYHAASGEEQATIERNPYTIFRQALKNCEPVIGLVPI-LRGGHFYQ
          GGNK.L..S.....L..VKRK.FEK.HAA..EEQATI..NPY.IF.QAL.N....IG.VPI....GHFYQ
Retrocopy GGNKLLPDS-SGCRLKGVKRKWFEK*HAAIPEEQATIQSNPYIIFHQALYN-*ALIGMVPIQYKCGHFYQ

Parental  VPVPLADRRRRFLAMKWMITECRKNKHRRTLMPEKLSHELLQA-FHNQGPVIKRKHEMHKMAEANRAL-A
          VP.P.ADR...FLAMK..ITEC.K..H..TL.PE.LSH.LLQA.FHN..P.I..KH.....AEAN.AL..
Retrocopy VPGPPADRCSHFLAMK*IITECQKTNHEWTLTPESLSHKLLQA<FHNYSPMIQTKHDRYTIAEANCAL<G

Parental  HYRWW
          HY.WW
Retrocopy HYLWW

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_1805 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1805 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 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009287	1 retrocopy	retro_amel_1444,
Canis familiaris	ENSCAFG00000004752	5 retrocopies	retro_cfam_2020, retro_cfam_2197, retro_cfam_438, retro_cfam_443, retro_cfam_540,
Callithrix jacchus	ENSCJAG00000014458	2 retrocopies	retro_cjac_290, retro_cjac_3316,
Erinaceus europaeus	ENSEEUG00000015775	1 retrocopy	retro_eeur_212,
Felis catus	ENSFCAG00000028759	2 retrocopies	retro_fcat_2013, retro_fcat_424,
Loxodonta africana	ENSLAFG00000002873	1 retrocopy	retro_lafr_945,
Macropus eugenii	ENSMEUG00000012264	1 retrocopy	retro_meug_1826,
Mustela putorius furo	ENSMPUG00000013928	1 retrocopy	retro_mputfur_976,
Procavia capensis	ENSPCAG00000015942	1 retrocopy	retro_pcap_327,
Pteropus vampyrus	ENSPVAG00000008433	3 retrocopies	retro_pvam_610, retro_pvam_615, retro_pvam_678,
Ictidomys tridecemlineatus	ENSSTOG00000015200	2 retrocopies	retro_itri_1805 , retro_itri_461,