RetrogeneDB ID: retro_dord_54

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_1441:87479..87809(+)
• Located in intron of: ENSDORG00000009192

Retrocopy information

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

Parental gene information

• Parental gene symbol: Btf3
• Ensembl ID: ENSDORG00000014031
• Aliases: None
• Description: basic transcription factor 3 [Source:MGI Symbol;Acc:MGI:1202875]

Sequence

>retro_dord_54
TCAGCAGATGACAAAAAACTCCAGTTCTCCTTAAAGAAGTTAGGCGTGAACAATATCTCTGGTATTGAGGAGGTGAATAT
GTTTACAAACCAAGGAACAGTGATCCACTTTAACAACTCTAAAGTTCAGGCATCTTCGGCAGCAAATACTTTCACCATTA
CAGGCCATGCTGACACAAAGCAGCTGACAGAAATGCTTCCCAGCATCTTGAACCAGCTTGGTGCAGACAGTCTGACTAGT
TTAAGGAGACTGGCTGAAGCTCTGCCCAAACAATCTGTGGATGAAAAAGCACCACTTGCTACTGGCGAGGATGATGATGA
TGAAGTTCCA

Alignment

ORF - retro_dord_54 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.45 %
• Parental protein coverage: 58.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TADDKKLQFSLKKLGVNNISGIEEVNMFTNQGTVIHFNNPKVQASLAANTFTITGHAETKQLTEMLPSIL
          .ADDKKLQFSLKKLGVNNISGIEEVNMFTNQGTVIHFNN.KVQAS.AANTFTITGHA.TKQLTEMLPSIL
Retrocopy SADDKKLQFSLKKLGVNNISGIEEVNMFTNQGTVIHFNNSKVQASSAANTFTITGHADTKQLTEMLPSIL

Parental  NQLGADSLTSLRRLAEALPKQSVDGKAPLATGEDDDDEVP
          NQLGADSLTSLRRLAEALPKQSVD.KAPLATGEDDDDEVP
Retrocopy NQLGADSLTSLRRLAEALPKQSVDEKAPLATGEDDDDEVP

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_54 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 6 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008212	3 retrocopies	retro_cfam_1660, retro_cfam_1741, retro_cfam_531,
Callithrix jacchus	ENSCJAG00000016600	4 retrocopies	retro_cjac_1454, retro_cjac_1673, retro_cjac_2640, retro_cjac_281,
Ciona savignyi	ENSCSAVG00000009653	1 retrocopy	retro_csav_25,
Dipodomys ordii	ENSDORG00000014031	5 retrocopies	retro_dord_287, retro_dord_341, retro_dord_422, retro_dord_54 , retro_dord_66,
Monodelphis domestica	ENSMODG00000001762	3 retrocopies	retro_mdom_189, retro_mdom_454, retro_mdom_931,
Otolemur garnettii	ENSOGAG00000013918	1 retrocopy	retro_ogar_46,