RetrogeneDB ID: retro_itri_683

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393310.1:12696362..12697303(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000002311
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RNF168
• Ensembl ID: ENSSTOG00000021829
• Aliases: None
• Description: ring finger protein 168, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:26661]

Sequence

>retro_itri_683
CTGGCAAGAAAGCTAAGCATTAACATTGATAATTTCTGCGAGGGGAGTACCTTGGCTTCTCCTTTGAATTCCAGAAAATC
TGATCCAGTCACAACCAAGTCACAAAAGAAAAATAAGAACCAACAAAGAAACATTGGAAATATTCAGAAGTATTTGTCAC
CTAAATCTCTATTTGGATCAGCAACACAGTCTGAAGTTGTACAAGAAGTCAGGAGAAACTCCACATTCTAAGGAAATTGA
CAGAAGTCATATGAAGAGCCCTACAGGGCAAGATACAGAAATTGAAGAAGATATGCCAAACACTTTCTCCTCAAATGTGC
CTTGAAATTCAAGAACAAGGTACAAAGTCTTCAGTAGAGTCACCTATGCCATGGTTATGTGTCTGTGACGCAGAACAGTG
CCTTGAAGGAAAAGCCAAAAGATCAAACAATCATGATCAAGAGTTATATGTCTTAAAGTATGAAGGACCTAAATCCAAAG
TTCCCTACTCTAAAGAAACTACAGTTAAGCCTTGTGGCAAGACAGAGAATGGGCGTACTTCTTCAAATATGATACAAATA
ATTGGAGACAGCCCAGTTGAGACAGAGTCTAGCCAACCAGACAGTCAAGGTGTTTCAAAAAGAAAAAGCCAGGAATCTTC
AGTTGAAGCAGTCAGAGATTCATGCTTTTCTTTAAAAAGGAAGAACAAGTTCTCAGAATCTTCTTCAGGTCAAGAGGAAA
CAGAAATGAATTTTACCCCAAAACTGATAGATTTGGAGCATTTACTTTTTGAGAGACACAAACAAGAAGAACAAGACCGG
CTATTAGCGTTACAACTGCAGAAAGAGGTGGATAAAGAACTAATGAAGCCAAACCGGCAAAAAGGATCCCCAGATGGGTA
CCAGTTACGTACTACATCCTCACCTCCACATAACTTACTAAATGGGCAGAAGAATTACAAA

Alignment

ORF - retro_itri_683 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.24 %
• Parental protein coverage: 55.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LARKLSININNFCEGSTLASPLNSRKSDPVTTKSQKKNKNKQRNIGNIQKYLSPKSLFGSATQSEVVQEV
          LARKLSINI.NFCEGSTLASPLNSRKSDPVTTKSQKKNKN.QRNIGNIQKYLSPKSLFGSATQSEVVQEV
Retrocopy LARKLSINIDNFCEGSTLASPLNSRKSDPVTTKSQKKNKNQQRNIGNIQKYLSPKSLFGSATQSEVVQEV

Parental  RRNST-TKEIDRSHMKSPTGQDTEIEEDMP-TLSPQMCLEIQEQGTKSSVESPMPWLCVYDAEQCLEGKA
          RRNST..KEIDRSHMKSPTGQDTEIEEDMP.TLSPQMCLEIQEQGTKSSVESPMPWLCV.DAEQCLEGKA
Retrocopy RRNST>SKEIDRSHMKSPTGQDTEIEEDMP>TLSPQMCLEIQEQGTKSSVESPMPWLCVCDAEQCLEGKA

Parental  KRSNNHDQELYVLQYEGPKTKVPYSKEATVKPCGKTENGRTSSNMIQIIGDNPVEIESSQPDSKGVSKRK
          KRSNNHDQELYVL.YEGPK.KVPYSKE.TVKPCGKTENGRTSSNMIQIIGD.PVE.ESSQPDS.GVSKRK
Retrocopy KRSNNHDQELYVLKYEGPKSKVPYSKETTVKPCGKTENGRTSSNMIQIIGDSPVETESSQPDSQGVSKRK

Parental  SQESSVEAVRDSCFSLKRKKKFSESSSDQEETEMNFTQKLIDLEHLLFERHKQEEQDRLLALQLQKEVDK
          SQESSVEAVRDSCFSLKRK.KFSESSS.QEETEMNFT.KLIDLEHLLFERHKQEEQDRLLALQLQKEVDK
Retrocopy SQESSVEAVRDSCFSLKRKNKFSESSSGQEETEMNFTPKLIDLEHLLFERHKQEEQDRLLALQLQKEVDK

Parental  ELMKPNRQKGSPDGYQLRTTSSPPHNLLNGQKNYK
          ELMKPNRQKGSPDGYQLRTTSSPPHNLLNGQKNYK
Retrocopy ELMKPNRQKGSPDGYQLRTTSSPPHNLLNGQKNYK

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_683 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_683 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
Bos taurus	ENSBTAG00000013317	1 retrocopy	retro_btau_1816,
Felis catus	ENSFCAG00000022131	1 retrocopy	retro_fcat_1967,
Loxodonta africana	ENSLAFG00000010864	1 retrocopy	retro_lafr_1181,
Myotis lucifugus	ENSMLUG00000012066	1 retrocopy	retro_mluc_1315,
Ictidomys tridecemlineatus	ENSSTOG00000021829	1 retrocopy	retro_itri_683 ,