RetrogeneDB ID: retro_itri_1248

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393411.1:2389115..2389528(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000028336
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PPIH
• Ensembl ID: ENSSTOG00000000115
• Aliases: None
• Description: peptidylprolyl isomerase H (cyclophilin H) [Source:HGNC Symbol;Acc:14651]

Sequence

>retro_itri_1248
GTGGCAAATTCAAGCTCTGTCAACACATTGTGTTCTTTGATGTCAGCTTTTTCAATCAGGAAGTTGGTCACATGAAGATA
CAGCTGTTTGCAGACATTGTACCTAAGACCACCAAGAACTTTAGGCAGTTCTGTACTGGAGAAATTCAGAAAAGATGGGG
TGCCCATAGGAAACAAAGGGGGAGCACCTTCCTCGTAGTCATAAAGGATTTCATGATTTAGGGTAGAGATATTGTTAATG
GAGGTAGTACTTGAGTTGTCAGTATTTACTTGGGGGCCATTTGCTGATGAAAAATTTAAACTTAGACACTTGGCTCCAGG
CCTCTTTCTATGGTAAGCAGTGGTCCCAGTACAAATAACCACCAGTTCTTCATCACATGCTATAAGTGTGATTGGCTTGG
TGGGAAGCATTTG

Alignment

ORF - retro_itri_1248 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.5 %
• Parental protein coverage: 77.4 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VANSSPVNP-VVFFDVSIGGQEVGRMKIELFADVVPKTAENFRQFCTGEFRKD-GVPIGYKGSTFHRVIK
          VANSS.VN...VFFDVS...QEVG.MKI.LFAD.VPKT..NFRQFCTGE..K..G......GSTF..VIK
Retrocopy VANSSSVNT<IVFFDVSFFNQEVGHMKIQLFADIVPKTTKNFRQFCTGEIQKRWGAHRKQRGSTFLVVIK

Parental  DFMIQGGDFVNGDGTGVASIYR-GPFADENFKLRHSAPGL-LSMANSGPSTNGCQFFITCSKCDWLDGKH
          DFMI.G.D.VNG..T.V.SIY..GPFADE.FKLRH.APGL.LSM..SGPSTN..QFFITC.KCDWL.GKH
Retrocopy DFMI*GRDIVNGGST*VVSIYL>GPFADEKFKLRHLAPGL<LSMVSSGPSTNNHQFFITCYKCDWLGGKH

Parental  V
          .
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_1248 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1248 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 19 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000526	1 retrocopy	retro_amel_1481,
Bos taurus	ENSBTAG00000004590	1 retrocopy	retro_btau_1530,
Callithrix jacchus	ENSCJAG00000003145	5 retrocopies	retro_cjac_129, retro_cjac_1886, retro_cjac_2205, retro_cjac_3120, retro_cjac_4110,
Cavia porcellus	ENSCPOG00000008214	8 retrocopies	retro_cpor_1511, retro_cpor_785, retro_cpor_786, retro_cpor_794, retro_cpor_795, retro_cpor_796, retro_cpor_797, retro_cpor_798,
Dipodomys ordii	ENSDORG00000016152	3 retrocopies	retro_dord_151, retro_dord_173, retro_dord_447,
Homo sapiens	ENSG00000171960	2 retrocopies	retro_hsap_4740, retro_hsap_928,
Gorilla gorilla	ENSGGOG00000022507	2 retrocopies	retro_ggor_2945, retro_ggor_748,
Macropus eugenii	ENSMEUG00000001691	1 retrocopy	retro_meug_1699,
Myotis lucifugus	ENSMLUG00000025400	2 retrocopies	retro_mluc_1922, retro_mluc_2243,
Macaca mulatta	ENSMMUG00000013129	1 retrocopy	retro_mmul_1124,
Mustela putorius furo	ENSMPUG00000013966	2 retrocopies	retro_mputfur_285, retro_mputfur_542,
Nomascus leucogenys	ENSNLEG00000012313	2 retrocopies	retro_nleu_1242, retro_nleu_289,
Oryctolagus cuniculus	ENSOCUG00000011453	1 retrocopy	retro_ocun_1195,
Procavia capensis	ENSPCAG00000011139	1 retrocopy	retro_pcap_81,
Pongo abelii	ENSPPYG00000001467	2 retrocopies	retro_pabe_3686, retro_pabe_797,
Pan troglodytes	ENSPTRG00000000614	2 retrocopies	retro_ptro_3155, retro_ptro_644,
Pteropus vampyrus	ENSPVAG00000005500	1 retrocopy	retro_pvam_107,
Ictidomys tridecemlineatus	ENSSTOG00000000115	2 retrocopies	retro_itri_1248 , retro_itri_412,
Tarsius syrichta	ENSTSYG00000003182	2 retrocopies	retro_tsyr_224, retro_tsyr_647,