RetrogeneDB ID: retro_ocun_1357

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 7:48604208..48604709(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DTD1
• Ensembl ID: ENSOCUG00000010988
• Aliases: None
• Description: D-tyrosyl-tRNA deacylase 1 [Source:HGNC Symbol;Acc:16219]

Sequence

>retro_ocun_1357
CACAGGGTCCGAAAGATTTTAAACCTGCGTGTGTTCGAGGACGAGAGTGGGAAGCACTGGTCGAAAAGCGTGATGGACAA
GCAGCATGAGGTGCTGTGCGTCAGCCAGTTTACCCTGCAGTGTGTCCTCAAGGGCAGCAAGCCCGACTTTCACCTGAAAG
CCATGCCCTCGGAGCAGGCAGAGGGCTTCTACAACAGCTTCCTGGAGCAGTTGCGGAAGGCGTACTGGCCGGAGCTCATC
AAAGATGGCAAGTTTGGTGCCTACATGCAAGTGCACATTCAGAACGACGGACCCGTGACCATAGAGCTGGAATCTCCGGC
ACCTGGCGCTGCTGCCTCTGACCCAAAGCAGCTATCCAAGCTTGAAAAACAACAGCAGAGGAAAGAAAAGACCCGAGCCA
AGGGACCCTCAGAGTCCAGCAAAGAAAGACCCGCACCCCGCAAGGAAAACCGCAGCGCCAGCAGCTGGGCCGAGGGTGAC
GTGTCCTCAGAGCGGGAGCCG

Alignment

ORF - retro_ocun_1357 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.41 %
• Parental protein coverage: 79.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HMVRKILNLRVFEDESGKHWSKSVMDKQYEVLCVSQFTLQCVLKGSKPDFHL-AMPSEQAEGFYNSFLEQ
          H.VRKILNLRVFEDESGKHWSKSVMDKQ.EVLCVSQFTLQCVLKGSKPDFHL.AMPSEQAEGFYNSFLEQ
Retrocopy HRVRKILNLRVFEDESGKHWSKSVMDKQHEVLCVSQFTLQCVLKGSKPDFHLKAMPSEQAEGFYNSFLEQ

Parental  LRKAYRPELIKDGKFGAYMQVHIQNDGPVTIELESPAPGAAASDPKQLSKLEKQQQRKEKTRAKGPSESS
          LRKAY.PELIKDGKFGAYMQVHIQNDGPVTIELESPAPGAAASDPKQLSKLEKQQQRKEKTRAKGPSESS
Retrocopy LRKAYWPELIKDGKFGAYMQVHIQNDGPVTIELESPAPGAAASDPKQLSKLEKQQQRKEKTRAKGPSESS

Parental  KERPAPRKEDRSASSGAEGDVSSEREP
          KERPAPRKE.RSASS.AEGDVSSEREP
Retrocopy KERPAPRKENRSASSWAEGDVSSEREP

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.17 RPM	18.87 RPM
SRP017611_kidney	0.00 RPM	17.74 RPM
SRP017611_liver	0.00 RPM	7.32 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1357 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1357 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1357 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000008964	1 retrocopy	retro_btau_767,
Macropus eugenii	ENSMEUG00000009170	2 retrocopies	retro_meug_137, retro_meug_1809,
Macaca mulatta	ENSMMUG00000012880	1 retrocopy	retro_mmul_217,
Monodelphis domestica	ENSMODG00000005696	1 retrocopy	retro_mdom_509,
Mus musculus	ENSMUSG00000027430	1 retrocopy	retro_mmus_2774,
Oryctolagus cuniculus	ENSOCUG00000010988	1 retrocopy	retro_ocun_1357 ,
Tupaia belangeri	ENSTBEG00000000242	1 retrocopy	retro_tbel_3434,