RetrogeneDB ID: retro_itri_562

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393301.1:4123078..4123528(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COMMD1
• Ensembl ID: ENSSTOG00000015062
• Aliases: None
• Description: copper metabolism (Murr1) domain containing 1 [Source:HGNC Symbol;Acc:23024]

Sequence

>retro_itri_562
ATCATGGAGGAGCTGTTATGGAGCCAACTCTATCTAGAGGGTTCCCTGGAGGAGTTCTGTCCCTTTCTGATGAAGATTCC
AGGATTCTTAAGTTGTCTTCATATGCAAACATAGATTTCAATTATCTGGAGATATTCTTGCTTGCTGAAACCCAAAAGTA
AGGCAGGAATGCATCTGACCAAGTTGCTGTCAATTCTAAATTCTGAAAGAGCCACAAGACAGAAATCTAAGAGAGCTTCT
TGAACAATAGCTGTTGAGACAACAGACTTTGGGGCCTGAGATGAAGAGGTGATGGTACATTAAGGCCCTCATCTCAAATA
TATACCCTTGTTGCCATATAAAGCTGGAACTCAGGAAAACTATACAGGGATCTGAATTTCTGTGTTTGAGATTTGATGAG
ATCAAGATCAAGTAAATCCTGAAGAAATTTTCCAAGTAGAAGAAAGTATA

Alignment

ORF - retro_itri_562 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.62 %
• Parental protein coverage: 81.38 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ITEELLRSQLYPEVSAEEFRPFLAKMRG-ILKSIASADMDFNQLEAFLTAQTKKQGGITSDQAAVISKFW
          I.EELL.SQLY.E.S.EEF.PFL.K..G.ILK....A..DFN.LE.FL.A.T.K.G...SDQ.AV.SKF.
Retrocopy IMEELLWSQLYLEGSLEEFCPFLMKIPG<ILKLSSYANIDFNYLEIFLLAETQK*GRNASDQVAVNSKF*

Parental  KSHKTKIRESLMNQSRWDNGLRGLSWRVDSKSQSRHSSQIHTPVAI-IELEFGKSGQESEFLCLEFDEIK
          KSHKT.I.ES..N.S..DN.L.GL..R.D.....R.SSQI.T.VAI.I.LE..K..Q.SEFLCL.FDEIK
Retrocopy KSHKTEI*ESFLNNSC*DNRLWGLR*RGD--GTLRPSSQIYTLVAI<IKLELRKTIQGSEFLCLRFDEIK

Parental  VNQILKKLS-EVEETI
          ...ILKK.S..VEE.I
Retrocopy IK*ILKKFS<QVEESI

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_562 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_562 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003090	1 retrocopy	retro_cfam_343,
Cavia porcellus	ENSCPOG00000002088	1 retrocopy	retro_cpor_482,
Mustela putorius furo	ENSMPUG00000005842	1 retrocopy	retro_mputfur_1120,
Ictidomys tridecemlineatus	ENSSTOG00000015062	1 retrocopy	retro_itri_562 ,
Tarsius syrichta	ENSTSYG00000000812	1 retrocopy	retro_tsyr_88,