RetrogeneDB ID: retro_dord_697

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_5791:6513..7024(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Pbk
• Ensembl ID: ENSDORG00000014896
• Aliases: None
• Description: PDZ binding kinase [Source:MGI Symbol;Acc:MGI:1289156]

Sequence

>retro_dord_697
GGTATTTTTACAATTAAAATAAAAAAGAAACTGCTTCATGGAGATATAAAGTCTTCAAATGTAATTAAAGGTGATTTCGA
AACAGTTAAAATCTGTGATGTAGAATTCTGTCTAACACTGGATGAAAATGTGACTGTGACTGATCCTGAGGCCTGTTATG
TTGGTACTGAGCCATGGAAACCCAAGGAAGCTTTGGAGGAAAAATGGCATTGTTACTGACAAAGCAGACATATTTGCCTT
TGGCCTAACACTTTGGGAAATGATGACCTTATCTATCCCACACATTAATCTCTCAGATGATGATGATGATGAAGATAAAG
CTTTTGATGAAAGTAACTTTGAGGATGAAGCATACTATGCTGTGTTGGGAACCAGACCACCTATTAATATTGAAGAACTG
AATGAGTCTTACCAGAAACTAATTGAACTCTTCTCTGTGTGCACCAATGAAGATCCGGAAGATCATCCTTCTGCTACTCA
GATTGTTGATGCTTTGGAGCTAGATGAGGAG

Alignment

ORF - retro_dord_697 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.97 %
• Parental protein coverage: 56.58 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GLKYLHQEKKLLHGDIKSSNVVIKGYFETVKICDVGVSLPLDENMTVTDPEACYIGTEPWKPKEALEE-N
          G.......KKLLHGDIKSSNV.IKG.FETVKICDV...L.LDEN.TVTDPEACY.GTEPWKPKEALEE.N
Retrocopy GIFTIKIKKKLLHGDIKSSNV-IKGDFETVKICDVEFCLTLDENVTVTDPEACYVGTEPWKPKEALEE>N

Parental  GIITDKADIFAFGLTLWEMMTLSIPHINLSDDDDDDEDKTFDESDFDDEAYYAALGTRPPINIEELDESY
          GI.TDKADIFAFGLTLWEMMTLSIPHINLSDDDDD.EDK.FDES.F.DEAYYA.LGTRPPINIEEL.ESY
Retrocopy GIVTDKADIFAFGLTLWEMMTLSIPHINLSDDDDD-EDKAFDESNFEDEAYYAVLGTRPPINIEELNESY

Parental  QKVIELFSVCTNEDPEDRPSAAQIVDALELDEE
          QK.IELFSVCTNEDPED.PSA.QIVDALELDEE
Retrocopy QKLIELFSVCTNEDPEDHPSATQIVDALELDEE

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_697 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021069	1 retrocopy	retro_btau_150,
Canis familiaris	ENSCAFG00000008369	1 retrocopy	retro_cfam_1694,
Dipodomys ordii	ENSDORG00000014896	1 retrocopy	retro_dord_697 ,
Myotis lucifugus	ENSMLUG00000009596	1 retrocopy	retro_mluc_713,
Monodelphis domestica	ENSMODG00000015986	1 retrocopy	retro_mdom_245,
Mus musculus	ENSMUSG00000022033	1 retrocopy	retro_mmus_2452,
Otolemur garnettii	ENSOGAG00000009887	1 retrocopy	retro_ogar_3495,
Tupaia belangeri	ENSTBEG00000002239	1 retrocopy	retro_tbel_3290,