RetrogeneDB ID: retro_ttru_552

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_2661:808440..808713(+)
• Located in intron of: ENSTTRG00000004555

Retrocopy information

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

Parental gene information

• Parental gene symbol: LYRM4
• Ensembl ID: ENSTTRG00000007073
• Aliases: None
• Description: LYR motif containing 4 [Source:HGNC Symbol;Acc:21365]

Sequence

>retro_ttru_552
ATTGCAGCCTCCAGCCACGCACGAGTGCTGGATATGTACCAGGCAATGCTGAGGGAGAGCAAGCACTTCAGTGCCGACAA
CTACAGAACTTACACCATCAGGAGGATAAGAGATGTCTTCAGAGAAAATAAGAATGTAAAGGATCCTGTAAAAATTCAAG
CCCTAATGAATAAAGCCAAAAGAGACCCTGGGATAATGCATAGACAGGTCCACATTGGCCAACTATATTTGACTGACAAG
CTTGTCAGTTAGAATCAAGAGAAGCCCAGGACC

Alignment

ORF - retro_ttru_552 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.22 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAASSRAQVLDLYRAMLRESKHFSAYNYRSYAIRRIRDAFRENKNVKDPVQIQALMNKAKRDLGIIRRQV
          .AASS.A.VLD.Y.AMLRESKHFSA.NYR.Y.IRRIRD.FRENKNVKDPV.IQALMNKAKRD.GI..RQV
Retrocopy IAASSHARVLDMYQAMLRESKHFSADNYRTYTIRRIRDVFRENKNVKDPVKIQALMNKAKRDPGIMHRQV

Parental  HIGQMYSTDKLIIENQEKPRT
          HIGQ.Y.TDKL...NQEKPRT
Retrocopy HIGQLYLTDKLVS*NQEKPRT

Legend:

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

Expression

RNA-Seq

Tursiops truncatus was not studied using RNA-Seq expression data.

ChIP-Seq

Tursiops truncatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ttru_552 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_552 was not experimentally validated.

Homology

Retrocopy orthology:

Tursiops truncatus 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 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000031432	1 retrocopy	retro_btau_783,
Callithrix jacchus	ENSCJAG00000021370	1 retrocopy	retro_cjac_1371,
Homo sapiens	ENSG00000214113	1 retrocopy	retro_hsap_194,
Macropus eugenii	ENSMEUG00000005958	1 retrocopy	retro_meug_656,
Myotis lucifugus	ENSMLUG00000028065	1 retrocopy	retro_mluc_394,
Mustela putorius furo	ENSMPUG00000000532	1 retrocopy	retro_mputfur_1459,
Mus musculus	ENSMUSG00000046573	1 retrocopy	retro_mmus_2374,
Nomascus leucogenys	ENSNLEG00000011472	1 retrocopy	retro_nleu_1002,
Rattus norvegicus	ENSRNOG00000047970	2 retrocopies	retro_rnor_1862, retro_rnor_2052,
Tursiops truncatus	ENSTTRG00000007073	1 retrocopy	retro_ttru_552 ,