RetrogeneDB ID: retro_dord_32

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_4079:8327..9020(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDORG00000005158
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDORG00000013766
• Aliases: None
• Description: None

Sequence

>retro_dord_32
ATGACCACCAACAAAAGTCCCTTGCATCCCTACTGGCCTCGGAACCTGAAGCTTGACAACTTTGTGCCTAATGACATTCC
CACCTGGCATATCCTAGCTGGCCTGTTCTCTGTCTCTGGAGCCCTAGTTTTGACCACATGGCTGTTATCCAATCGTACTT
CAGTTGCCCCACTGGGAACTTGGCGGAAACTGTCCTTGTGCTGGTTTGCAGTATGTGCATTCATTCACTTGGTGATTGAG
GGGTGGTTCAGTTTCTACAACAAGACTCTTCTTAGAGACCAAGACTTTTTATCCCAACTCTGGAAAGAGTATTCCAAGGG
AGACAGCTGTTACATCATTTGGGACAACTTTATCATTTGTATGGAGACCATCACAGCTAGCATGTGGGGACCACTCAGCC
TGTGGGTAGTGATTGCCTTTTTCCGCCAACAACCAGTTTGTTATGTTCTACAGCTCGTGGTTTCTCTGGGCCAGATCTAT
GGAGATGTTCTGTACTTCCTGACGGAGTATGGAGATGAATTCCAGCATTCGGAGATGGGCCACCCAGTCTATTTCTGGTT
TTATTTTGTCTTCATGAATAGCTTATGGCTGGTGATACCTAGAATCCTCTTGCTCGATTTTGTGAAGCAGCTTACTCATG
CTCAGAGTATGTTGGACTCCAGAGTAACAAAAGCCAAGAGGAAGTTAAACTAA

Alignment

ORF - retro_dord_32 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.7 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KEYSKGDSRYIICDNFIVCMETITASMWGPLSLWVVIAFLRQQPVRYVLQLIVSLGQIYGDVLYFLTEYR
          KEYSKGDS.YII.DNFI.CMETITASMWGPLSLWVVIAF.RQQPV.YVLQL.VSLGQIYGDVLYFLTEY.
Retrocopy KEYSKGDSCYIIWDNFIICMETITASMWGPLSLWVVIAFFRQQPVCYVLQLVVSLGQIYGDVLYFLTEYG

Parental  DEFQHSEMGHPVYFWFYFVFMNALWLVIPGILLLDSVKQLSHVQSMLDSRVTKAKRKLN
          DEFQHSEMGHPVYFWFYFVFMN.LWLVIP.ILLLD.VKQL.H.QSMLDSRVTKAKRKLN
Retrocopy DEFQHSEMGHPVYFWFYFVFMNSLWLVIPRILLLDFVKQLTHAQSMLDSRVTKAKRKLN

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_32 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009287	1 retrocopy	retro_btau_1337,
Dipodomys ordii	ENSDORG00000013766	1 retrocopy	retro_dord_32 ,
Otolemur garnettii	ENSOGAG00000016187	3 retrocopies	retro_ogar_1190, retro_ogar_1191, retro_ogar_1942,
Procavia capensis	ENSPCAG00000009202	1 retrocopy	retro_pcap_218,