RetrogeneDB ID: retro_itri_1133

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393383.1:995016..995192(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C15orf48
• Ensembl ID: ENSSTOG00000021929
• Aliases: None
• Description: chromosome 15 open reading frame 48 [Source:HGNC Symbol;Acc:29898]

Sequence

>retro_itri_1133
ATTATTCCTTTGGTTCTGATCATGATTGTTGCAGTTAGTAGACCCTCATCTTTTGCTGTATACACCTTTTGAAAAACCAT
TGTAATATTCATTGAAAAAAGAAATCCAGAATCTTGGGAAAATGTGGATCCTATTATATCTCAGGGTTTATAATAATAAA
CCAACAATAGGAGCCC

Alignment

ORF - retro_itri_1133 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.0 %
• Parental protein coverage: 83.1 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LIPLVFFMTFAAAGASSFAIYSLKKTDVILDRKRNPEPWEAVDPSEPQKL-ITINQQWKP
          .IPLV..M..A....SSFA.Y...KT.VI...KRNPE.WE.VDP...Q.L.I.INQQ..P
Retrocopy IIPLVLIMIVAVSRPSSFAVYTF*KTIVIFIEKRNPESWENVDPIISQGL<IIINQQ*EP

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_1133 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1133 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 9 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000031501	2 retrocopies	retro_cfam_1654, retro_cfam_669,
Cavia porcellus	ENSCPOG00000020706	1 retrocopy	retro_cpor_450,
Erinaceus europaeus	ENSEEUG00000003556	1 retrocopy	retro_eeur_594,
Macropus eugenii	ENSMEUG00000013137	4 retrocopies	retro_meug_1593, retro_meug_2033, retro_meug_278, retro_meug_63,
Monodelphis domestica	ENSMODG00000028279	1 retrocopy	retro_mdom_225,
Oryctolagus cuniculus	ENSOCUG00000029216	1 retrocopy	retro_ocun_33,
Rattus norvegicus	ENSRNOG00000050251	1 retrocopy	retro_rnor_484,
Sarcophilus harrisii	ENSSHAG00000006433	3 retrocopies	retro_shar_296, retro_shar_416, retro_shar_744,
Ictidomys tridecemlineatus	ENSSTOG00000021929	1 retrocopy	retro_itri_1133 ,