RetrogeneDB ID: retro_itri_1296

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393430.1:3925800..3926170(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CYB5B
• Ensembl ID: ENSSTOG00000011316
• Aliases: None
• Description: cytochrome b5 type B (outer mitochondrial membrane) [Source:HGNC Symbol;Acc:24374]

Sequence

>retro_itri_1296
TATTGGTTGAAGGAGGTGAGGAAGGGCAACTCCTCGAAAGAACTATAGCTGGTGGTCTGCGGGAGAGTCCACGATATCAC
CAGTTCCTCAATGAGCATCCTGGTGGAGAAGAGATTCTGCTAGAACAAGCTGGTACAGATTCATCTGAAAGCTTTGAATA
TGGAGACAATTTCTCTGATGCCAGAGAAAAGCTAAAGCAATGCTACATCAGTGACGTCCATCCGAGTGACCTCAAACCTG
AGGAGGTAACAAGGATCCTTCGAAAAATGATACATGCAAAAGGTGCTGGGCATATTGGACTTTCCCCATCATAGGTGCTA
TTCTCCTAGATTTCCTGTGTGGTTACTAAATGGTGGAAAGCAAATCCTCC

Alignment

ORF - retro_itri_1296 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.38 %
• Parental protein coverage: 88.65 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YRLEEVTKRNSSKELWLVIHGRVYDIT-RFLNEHPGGEEVLLEQAGTDSTESFEDVGHSSDAREMLKQYY
          Y.L.EV.K.NSSKEL.LV..GRV.DIT..FLNEHPGGEE.LLEQAGTDS.ESFE.....SDARE.LKQ.Y
Retrocopy YWLKEVRKGNSSKEL*LVVCGRVHDIT<QFLNEHPGGEEILLEQAGTDSSESFEYGDNFSDAREKLKQCY

Parental  IGDVHPSDLKPE-GGNKLLVTSTSHISSCWAYWIF---PIIGAILVGFLYRYYMAESKSS
          I.DVHPSDLKPE.GGNK......S....C...W.....PIIGAIL..FL..Y.M.ESKSS
Retrocopy ISDVHPSDLKPE<GGNK----DPSKNDTCKRCWAYWTFPIIGAILLDFLCGY*MVESKSS

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_1296 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1296 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 15 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Anas platyrhynchos	ENSAPLG00000007518	1 retrocopy	retro_apla_13,
Cavia porcellus	ENSCPOG00000014234	1 retrocopy	retro_cpor_1117,
Felis catus	ENSFCAG00000024541	1 retrocopy	retro_fcat_1816,
Gallus gallus	ENSGALG00000000660	1 retrocopy	retro_ggal_13,
Meleagris gallopavo	ENSMGAG00000008619	1 retrocopy	retro_mgal_12,
Myotis lucifugus	ENSMLUG00000006608	1 retrocopy	retro_mluc_1734,
Macaca mulatta	ENSMMUG00000012039	1 retrocopy	retro_mmul_128,
Mus musculus	ENSMUSG00000031924	1 retrocopy	retro_mmus_2289,
Oryctolagus cuniculus	ENSOCUG00000007729	2 retrocopies	retro_ocun_141, retro_ocun_255,
Pteropus vampyrus	ENSPVAG00000015984	1 retrocopy	retro_pvam_977,
Sarcophilus harrisii	ENSSHAG00000014200	1 retrocopy	retro_shar_688,
Ictidomys tridecemlineatus	ENSSTOG00000011316	1 retrocopy	retro_itri_1296 ,
Ictidomys tridecemlineatus	ENSSTOG00000022436	1 retrocopy	retro_itri_1617,
Tursiops truncatus	ENSTTRG00000010016	1 retrocopy	retro_ttru_521,
Drosophila melanogaster	FBgn0029854	1 retrocopy	retro_dmel_39,