RetrogeneDB ID: retro_itri_350

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393285.1:16812453..16812775(-)
• Located in intron of: ENSSTOG00000027189

Retrocopy information

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

Parental gene information

• Parental gene symbol: CNEP1R1
• Ensembl ID: ENSSTOG00000001179
• Aliases: None
• Description: CTD nuclear envelope phosphatase 1 regulatory subunit 1 [Source:HGNC Symbol;Acc:26759]

Sequence

>retro_itri_350
CGAAGACTTTGTGAATCCATTCAGCCTTTGTCTCCTGCTCCAGGATCCTGGAGAATGCTTCTCATGGAGGCATGTCTCTG
CCTAGGTGCCTGGAACGAGTTAATAGATCCCGAGACACCAAAAGGTCCTTCTTTGCATCTTTATGGAGTCGTGCCATTTT
TTACCATTAGCTTTTCACTCTAATAGGTTTATTCTTTGCTGGGTACACAAGAGAGTAGTTGTGCCATCAATTATAGCAGC
TCAATGTCAAACAGCATTAGCAGAGTATAAACACGTCCGTGATGATACAGGGAAACCAATTTTGAAATCTAGGCCTTCTG
TT

Alignment

ORF - retro_itri_350 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.79 %
• Parental protein coverage: 88. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RRLTEYIHCLQPATGRWRMLLIVVSVCTATGAWNWLIDPETQKV-SFFTSLWNH-PFFTIS-CITLIGLF
          RRL.E.I..L.PA.G.WRMLL.....C...GAWN.LIDPET.K..SFF.SLW...PFFTIS...TLIGLF
Retrocopy RRLCESIQPLSPAPGSWRMLLM--EACLCLGAWNELIDPETPKG<SFFASLWSR>PFFTIS<LFTLIGLF

Parental  FAG-IHKRVVAPSIIAARCRTVLAEYNMSCDDTGKLILKPRPHV
          FAG..HKRVV.PSIIAA.C.T.LAEY....DDTGK.ILK.RP.V
Retrocopy FAG<VHKRVVVPSIIAAQCQTALAEYKHVRDDTGKPILKSRPSV

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_350 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_350 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 17 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006491	1 retrocopy	retro_amel_732,
Callithrix jacchus	ENSCJAG00000001997	1 retrocopy	retro_cjac_4204,
Cavia porcellus	ENSCPOG00000012791	1 retrocopy	retro_cpor_669,
Erinaceus europaeus	ENSEEUG00000005737	1 retrocopy	retro_eeur_211,
Felis catus	ENSFCAG00000023936	1 retrocopy	retro_fcat_1713,
Homo sapiens	ENSG00000205423	1 retrocopy	retro_hsap_4886,
Gorilla gorilla	ENSGGOG00000025211	1 retrocopy	retro_ggor_3051,
Loxodonta africana	ENSLAFG00000012573	1 retrocopy	retro_lafr_907,
Myotis lucifugus	ENSMLUG00000006900	2 retrocopies	retro_mluc_1437, retro_mluc_2115,
Macaca mulatta	ENSMMUG00000008365	3 retrocopies	retro_mmul_1586, retro_mmul_1873, retro_mmul_2624,
Mustela putorius furo	ENSMPUG00000003109	1 retrocopy	retro_mputfur_453,
Nomascus leucogenys	ENSNLEG00000000727	2 retrocopies	retro_nleu_1341, retro_nleu_831,
Oryctolagus cuniculus	ENSOCUG00000005923	1 retrocopy	retro_ocun_1267,
Otolemur garnettii	ENSOGAG00000015665	1 retrocopy	retro_ogar_2835,
Pongo abelii	ENSPPYG00000007335	3 retrocopies	retro_pabe_1396, retro_pabe_2430, retro_pabe_3799,
Pan troglodytes	ENSPTRG00000041682	1 retrocopy	retro_ptro_3255,
Ictidomys tridecemlineatus	ENSSTOG00000001179	1 retrocopy	retro_itri_350 ,