RetrogeneDB ID: retro_itri_1468

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393498.1:1746575..1747114(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000019938
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000011496
• Aliases: None
• Description: None

Sequence

>retro_itri_1468
GTGTTCAAGAAATATGATGAAAAAGAAAATGTGTCCAATGGCATTCAGTTCAAAACATCATTTATTAAGGTCATTGAGAA
CCAATCGATAGGACAATTTTCAAGTACTGAACCGTGGCTTAATCAAATCATGCCTAAGAGCAAGCCTGTCAAAATAGTCC
AATGCCATGAACAGACAGAAATCTTTACAGTAAATGGAGAATCGCTATTTTTTAAACAAGGAGAAGGGCCTTTTTATCCA
ACTCTAAGTTTACTTCACAAATATCCTTTTATTCTGCCACACCAGCAGGTTGATAAAGGCGCCATCAAATTTGTACTCAG
TGGAGGAAAATCAGGTATCGAGGCTTAACTTCTCCTGGAGCTAAGCTTTACCCTGCTGCAGTAGCTACCACTGTTTCAAT
CATGGCAGAAGGCAAAGAGCATGCTCTGTGTGTTGGAGTCAAGATGATGTCTGCAGAAGACACTGAGAAAGTCAGCAAAG
GCATTGGCATTGAAAATATCCATTATTTAAATGATGAGCTGTGGCATATGAAGACATAC

Alignment

ORF - retro_itri_1468 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.56 %
• Parental protein coverage: 99.45 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MFKKFDEKENVSNCIQLKTSVIKGIKNQLIEQFPGIEPWLNQIMPKKDPVKIVRCHEHIEILTVNGELLF
          .FKK.DEKENVSN.IQ.KTS.IK.I.NQ.I.QF...EPWLNQIMPK..PVKIV.CHE..EI.TVNGE.LF
Retrocopy VFKKYDEKENVSNGIQFKTSFIKVIENQSIGQFSSTEPWLNQIMPKSKPVKIVQCHEQTEIFTVNGESLF

Parental  FRQREGPFYPTLRLLHKYPFILPHQQVDKGAIKFVLSGA-NIMCPGLTSPGAKLYPAAVDTIVAIMAEGK
          F.Q.EGPFYPTL.LLHKYPFILPHQQVDKGAIKFVLSG...I...GLTSPGAKLYPAAV.T.V.IMAEGK
Retrocopy FKQGEGPFYPTLSLLHKYPFILPHQQVDKGAIKFVLSGG<KIRYRGLTSPGAKLYPAAVATTVSIMAEGK

Parental  QHALCVGVMKMSAEDIEKVNKGIGIENIHYLNDGLWHMKTY
          .HALCVGV..MSAED.EKV.KGIGIENIHYLND.LWHMKTY
Retrocopy EHALCVGVKMMSAEDTEKVSKGIGIENIHYLNDELWHMKTY

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_1468 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1468 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 26 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000034992	1 retrocopy	retro_btau_116,
Canis familiaris	ENSCAFG00000018545	1 retrocopy	retro_cfam_94,
Cavia porcellus	ENSCPOG00000005502	1 retrocopy	retro_cpor_1411,
Equus caballus	ENSECAG00000014597	1 retrocopy	retro_ecab_697,
Erinaceus europaeus	ENSEEUG00000007258	1 retrocopy	retro_eeur_197,
Echinops telfairi	ENSETEG00000015462	1 retrocopy	retro_etel_19,
Felis catus	ENSFCAG00000008448	2 retrocopies	retro_fcat_1009, retro_fcat_310,
Homo sapiens	ENSG00000232119	1 retrocopy	retro_hsap_2422,
Gorilla gorilla	ENSGGOG00000009420	1 retrocopy	retro_ggor_1507,
Macropus eugenii	ENSMEUG00000014328	1 retrocopy	retro_meug_1518,
Myotis lucifugus	ENSMLUG00000015101	1 retrocopy	retro_mluc_16,
Macaca mulatta	ENSMMUG00000009043	1 retrocopy	retro_mmul_626,
Monodelphis domestica	ENSMODG00000010354	1 retrocopy	retro_mdom_203,
Mustela putorius furo	ENSMPUG00000001407	1 retrocopy	retro_mputfur_98,
Mus musculus	ENSMUSG00000000355	3 retrocopies	retro_mmus_2504, retro_mmus_2505, retro_mmus_69,
Nomascus leucogenys	ENSNLEG00000015021	1 retrocopy	retro_nleu_2442,
Oryctolagus cuniculus	ENSOCUG00000014315	1 retrocopy	retro_ocun_212,
Pongo abelii	ENSPPYG00000020687	2 retrocopies	retro_pabe_1786, retro_pabe_1833,
Pan troglodytes	ENSPTRG00000022241	1 retrocopy	retro_ptro_1396,
Pteropus vampyrus	ENSPVAG00000013249	3 retrocopies	retro_pvam_1323, retro_pvam_645, retro_pvam_867,
Rattus norvegicus	ENSRNOG00000002563	2 retrocopies	retro_rnor_1841, retro_rnor_957,
Ictidomys tridecemlineatus	ENSSTOG00000011496	2 retrocopies	retro_itri_1136, retro_itri_1468 ,
Tupaia belangeri	ENSTBEG00000010666	2 retrocopies	retro_tbel_1485, retro_tbel_4265,
Tarsius syrichta	ENSTSYG00000001440	1 retrocopy	retro_tsyr_55,
Tursiops truncatus	ENSTTRG00000007208	1 retrocopy	retro_ttru_1587,
Vicugna pacos	ENSVPAG00000001801	1 retrocopy	retro_vpac_138,