RetrogeneDB ID: retro_itri_1754

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393719.1:266833..267259(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000019887
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ARF1
• Ensembl ID: ENSSTOG00000009288
• Aliases: None
• Description: ADP-ribosylation factor 1 [Source:HGNC Symbol;Acc:652]

Sequence

>retro_itri_1754
ATGGGGAATATCTTTGCAAATCTCTTCAAGGGCCTTTTTGGGAAAAAAGAAATGCACATCCCCATGGTGGGCCTGGATGC
TGCAGGGAAGATGACGATTTTGTACAAACTGAAGCTGGGTCAAATTGTGACCGCCATTCCCACCATAGGTTTTAATGTGG
AGTACAAGAACATCAGCTTCCCTGTGTGGGACGTGGGTGGCCAAGACAAGATCCAGCTGCTAAGGCGCCACTACTTCCAG
AATACCCTTGGCTTGATCTTTGTGGTGGACAGCAATGACAGAGAGCGTGTGAATGAGGCCTTCGAGGAGCTCATGAGGAT
GCTGGCTGAGGATGAGCTGTGGGACACCGTCCTCCTGGTGTTTGCCAACAAGCAGGACCTCCCAAATGCCATGAACGTGG
CCAAAATCACAGATAAGCTGGGGCTG

Alignment

ORF - retro_itri_1754 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.59 %
• Parental protein coverage: 80.11 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGNIFANLFKGLFGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGG
          MGNIFANLFKGLFGKKEM.I.MVGLDAAGK.TILYKLKLG.IVT.IPTIGFN...VEYKNISF.VWDVGG
Retrocopy MGNIFANLFKGLFGKKEMHIPMVGLDAAGKMTILYKLKLGQIVTAIPTIGFN---VEYKNISFPVWDVGG

Parental  QDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEIT
          QDKI..L.RHYFQNT.GLIFVVDSNDRERVNEA.EELMRMLAEDEL.D.VLLVFANKQDLPNAMN.A.IT
Retrocopy QDKIQLLRRHYFQNTLGLIFVVDSNDRERVNEAFEELMRMLAEDELWDTVLLVFANKQDLPNAMNVAKIT

Parental  DKLGL
          DKLGL
Retrocopy DKLGL

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_1754 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1754 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 22 parental genes, and 54 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007725	2 retrocopies	retro_btau_1257, retro_btau_1390,
Callithrix jacchus	ENSCJAG00000016671	10 retrocopies	retro_cjac_1295, retro_cjac_1691, retro_cjac_1719, retro_cjac_2189, retro_cjac_2896, retro_cjac_300, retro_cjac_3181, retro_cjac_3311, retro_cjac_3335, retro_cjac_390,
Ciona savignyi	ENSCSAVG00000007011	1 retrocopy	retro_csav_2,
Ficedula albicollis	ENSFALG00000001088	1 retrocopy	retro_falb_2,
Gallus gallus	ENSGALG00000005393	1 retrocopy	retro_ggal_7,
Latimeria chalumnae	ENSLACG00000019009	1 retrocopy	retro_lcha_10,
Myotis lucifugus	ENSMLUG00000007020	6 retrocopies	retro_mluc_1631, retro_mluc_242, retro_mluc_2605, retro_mluc_428, retro_mluc_511, retro_mluc_876,
Macaca mulatta	ENSMMUG00000002792	3 retrocopies	retro_mmul_237, retro_mmul_541, retro_mmul_810,
Oryctolagus cuniculus	ENSOCUG00000023645	2 retrocopies	retro_ocun_1137, retro_ocun_247,
Otolemur garnettii	ENSOGAG00000010974	4 retrocopies	retro_ogar_2431, retro_ogar_295, retro_ogar_3353, retro_ogar_974,
Procavia capensis	ENSPCAG00000014202	2 retrocopies	retro_pcap_15, retro_pcap_23,
Pongo abelii	ENSPPYG00000000148	3 retrocopies	retro_pabe_3159, retro_pabe_849, retro_pabe_965,
Pelodiscus sinensis	ENSPSIG00000009767	1 retrocopy	retro_psin_12,
Sarcophilus harrisii	ENSSHAG00000014599	3 retrocopies	retro_shar_106, retro_shar_462, retro_shar_725,
Ictidomys tridecemlineatus	ENSSTOG00000004295	1 retrocopy	retro_itri_175,
Ictidomys tridecemlineatus	ENSSTOG00000009288	3 retrocopies	retro_itri_1754 , retro_itri_273, retro_itri_363,
Ictidomys tridecemlineatus	ENSSTOG00000013990	1 retrocopy	retro_itri_659,
Ictidomys tridecemlineatus	ENSSTOG00000019470	2 retrocopies	retro_itri_1439, retro_itri_1614,
Ictidomys tridecemlineatus	ENSSTOG00000019768	1 retrocopy	retro_itri_883,
Taeniopygia guttata	ENSTGUG00000000233	1 retrocopy	retro_tgut_2,
Tetraodon nigroviridis	ENSTNIG00000011685	1 retrocopy	retro_tnig_19,
Vicugna pacos	ENSVPAG00000003224	4 retrocopies	retro_vpac_281, retro_vpac_328, retro_vpac_6, retro_vpac_78,