RetrogeneDB ID: retro_ttru_175

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_1487:534223..534860(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FXN
• Ensembl ID: ENSTTRG00000010336
• Aliases: None
• Description: frataxin [Source:HGNC Symbol;Acc:3951]

Sequence

>retro_ttru_175
ATGTGGATGCTTGGGCGCCGAGCGGCCGCCAGCCTCTTGCCCCGCTCGGCGCCTCCGGGCTCTGCCTAGGCCCGCGCCGG
GGCCCCGCGGCCAACGAAGGACCCCCAGCTCTACGGCTGCCGGGGCCTGCGCACCGGGACCGCCGCGGCCGGCACACCCA
GCCAGCCCAGTCTGAGTCTCTGCTGCCTCAACCGGATCCTGAATGTCAAAAAGCAGTGTGTCTGTTGGATGAATTTGAGG
ACAACGGGAACTTTGGGTGACGCTGGCCCTCAGGACAATACCGCCTATGAAAGACTGGCCGAGGAGACGCTGGACTCCTT
AGCAGAGTTTTTTTGAAGACCTTGCAGACAAACCTTACACATTTGAAGACTATGATGTCTCCTTTGGGAGTGGTGTTTTA
AGAATTAAACTGGGTGGAGATCTAGGAACGTACGTCATCAACAAGTAGACCACAAACGAGCAAATCTGGTTGTCTTCACC
ATCCAGTGTCCGCAAGCGTTACGACTGGACTGGGAGAAACTGGGTGTACTCCCACGACGGTGTGTCCCTCCACGAGCTGC
TGGCCACAGAGCTGACTCAAGCCTTAAAAACCAAACTGGACTTATGTTCTCTGGCCTACTCTGGAAAAGGCACTTGC

Alignment

ORF - retro_ttru_175 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.67 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MWTLGRRAAASLLPRSAPPGSAQARAGAPRPTKDSRLYGCRGLRTGTAAAGTPSQPSLSLCCLNQMLNVK
          MW.LGRRAAASLLPRSAPPGSA.ARAGAPRPTKD..LYGCRGLRTGTAAAGTPSQPSLSLCCLN..LNVK
Retrocopy MWMLGRRAAASLLPRSAPPGSA*ARAGAPRPTKDPQLYGCRGLRTGTAAAGTPSQPSLSLCCLNRILNVK

Parental  KQWVCWMNLRTTGTLGDAGPLDDTTYERLVEETLDSLAE-FFEDLADKPYTCEDYDVSFVSGVLTIKLGG
          KQ.VCWMNLRTTGTLGDAGP.D.T.YERL.EETLDSLAE.FFEDLADKPYT.EDYDVSF.SGVL.IKLGG
Retrocopy KQCVCWMNLRTTGTLGDAGPQDNTAYERLAEETLDSLAE>FFEDLADKPYTFEDYDVSFGSGVLRIKLGG

Parental  DLGTYVINKQTPNKQIWLSSPSG-PKRYDWTGRNWVYSHDGVSLHELLATELTQALKTKLDLSSLAYSGK
          DLGTYVINK.T.N.QIWLSSPS...KRYDWTGRNWVYSHDGVSLHELLATELTQALKTKLDL.SLAYSGK
Retrocopy DLGTYVINK*TTNEQIWLSSPSSVRKRYDWTGRNWVYSHDGVSLHELLATELTQALKTKLDLCSLAYSGK

Parental  GTC
          GTC
Retrocopy GTC

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_175 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_175 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 13 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006915	1 retrocopy	retro_amel_1496,
Choloepus hoffmanni	ENSCHOG00000005107	2 retrocopies	retro_chof_349, retro_chof_94,
Callithrix jacchus	ENSCJAG00000001695	4 retrocopies	retro_cjac_1562, retro_cjac_1927, retro_cjac_3939, retro_cjac_813,
Dasypus novemcinctus	ENSDNOG00000024066	3 retrocopies	retro_dnov_2204, retro_dnov_2317, retro_dnov_307,
Equus caballus	ENSECAG00000019174	1 retrocopy	retro_ecab_311,
Homo sapiens	ENSG00000165060	2 retrocopies	retro_hsap_1447, retro_hsap_4311,
Gorilla gorilla	ENSGGOG00000007636	3 retrocopies	retro_ggor_1112, retro_ggor_2203, retro_ggor_2881,
Macaca mulatta	ENSMMUG00000000357	2 retrocopies	retro_mmul_2038, retro_mmul_826,
Mustela putorius furo	ENSMPUG00000009619	2 retrocopies	retro_mputfur_501, retro_mputfur_803,
Mus musculus	ENSMUSG00000059363	2 retrocopies	retro_mmus_1571, retro_mmus_3058,
Otolemur garnettii	ENSOGAG00000031105	2 retrocopies	retro_ogar_1865, retro_ogar_476,
Rattus norvegicus	ENSRNOG00000015213	1 retrocopy	retro_rnor_2276,
Tursiops truncatus	ENSTTRG00000010336	4 retrocopies	retro_ttru_1281, retro_ttru_175 , retro_ttru_546, retro_ttru_831,