RetrogeneDB ID: retro_dord_553

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_31177:4717..5078(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Plgrkt
• Ensembl ID: ENSDORG00000000109
• Aliases: None
• Description: plasminogen receptor, C-terminal lysine transmembrane protein [Source:MGI Symbol;Acc:MGI:1915009]

Sequence

>retro_dord_553
CTGGAAAGGCAGCTCCTGATGCAGAAAGAGATGAGGGAACGACAAATGGCCATGCAAATCCCTTGGTCTCGAGAATTCCT
CAAATATTTTGGCACTTTCTTTGGTATTGCAACCATCTCTTTAACAGAGGGAGCTATAAAACGAAAAAAAGCCAGCCTTC
CTCTTTCCCATTGTTCCGTTAAGTTTTATCTTCACCTACCAGTATGACTTGGGCTATGGAACACTCCTACAAAGAATGAA
AGGCGAAGCTGAAGACATACTGGAAACAGAAAAGACTAAGTTGCAGCTTCCCAAGGGAATAATCACTTTTGACAGCCTCG
AAAAGGCCAGGAGAGACCAGAGTAGTTTCTTCATAGACAAA

Alignment

ORF - retro_dord_553 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.04 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LERQLLMQNEMRERQMAMQIAWSREFLKYFGTFFGIATISLTAGAIKR-KKPAFLFPIVPLSFIFTYQYD
          LERQLLMQ.EMRERQMAMQI.WSREFLKYFGTFFGIATISLT.GAIKR.KKPAFLFPIVPLSFIFTYQYD
Retrocopy LERQLLMQKEMRERQMAMQIPWSREFLKYFGTFFGIATISLTEGAIKR>KKPAFLFPIVPLSFIFTYQYD

Parental  LGYGTLLQRMK-EAEDILETEKTKLQLPKGIITFDSLEKARRDQSS-FIDK
          LGYGTLLQRMK.EAEDILETEKTKLQLPKGIITFDSLEKARRDQSS.FIDK
Retrocopy LGYGTLLQRMKGEAEDILETEKTKLQLPKGIITFDSLEKARRDQSSFFIDK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Dipodomys ordii was not studied using RNA-Seq expression data.

ChIP-Seq

Dipodomys ordii was not studied using ChIP-Seq data.

EST

Dipodomys ordii was not studied using EST data.

TSS

Dipodomys ordii was not studied using FANTOM5 data.

Lab

retro_dord_553 was not experimentally validated.

Homology

Retrocopy orthology:

Dipodomys ordii 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000004320	1 retrocopy	retro_dnov_1300,
Dipodomys ordii	ENSDORG00000000109	1 retrocopy	retro_dord_553 ,
Otolemur garnettii	ENSOGAG00000003280	1 retrocopy	retro_ogar_2243,
Sarcophilus harrisii	ENSSHAG00000001757	1 retrocopy	retro_shar_822,