RetrogeneDB ID: retro_ttru_279

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_1761:419235..419507(-)
• Located in intron of: ENSTTRG00000001348

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP5G1
• Ensembl ID: ENSTTRG00000008526
• Aliases: None
• Description: ATP synthase, H+ transporting, mitochondrial Fo complex, subunit C1 (subunit 9) [Source:HGNC Symbol;Acc:841]

Sequence

>retro_ttru_279
GTGCACACCACTAGGACACTGTTTGTTCCTCTGGCTCTGATCCATTGTTGTGCCTGGGGTCTAATCAGGCCTGTGTCTGC
CTCCTTCCAAGCAGGCCAGAAATCCCATCTAAACAGCCTTTCTATAGCAGCTCCCCACAGGAGTTCCATACCAGTGTTGT
CTCCCAGGACACTGACCCAGCAGCCAAGCTTATTGCTGGTGGGGACACCACAGTTGGTATGGCTGGTTCAGAGGCCAGCA
TTAGAACAGTGTTTGACAGATTGATGCTTGGG

Alignment

ORF - retro_ttru_279 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.35 %
• Parental protein coverage: 69.23 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MQTTRALLIPPALIRSCTRGLSRPVSASFL-SRPPSYSSVPL-QVARREFQTSVVSRDIDTAAKFIGAGA
          ..TTR.L..P.ALI..C..GL.RPVSASF..SRP...S..P.......EF.TSVVS.D.D.AAK.I..G.
Retrocopy VHTTRTLFVPLALIHCCAWGLIRPVSASFQ<SRPEIPSKQPFYSSSPQEFHTSVVSQDTDPAAKLIAGGD

Parental  ATVGVAGSGAGIGTVFGSLIIG
          .TVG.AGS.A.I.TVF..L..G
Retrocopy TTVGMAGSEASIRTVFDRLMLG

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_279 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_279 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 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000006341	1 retrocopy	retro_acar_9,
Bos taurus	ENSBTAG00000018339	3 retrocopies	retro_btau_1506, retro_btau_423, retro_btau_431,
Callithrix jacchus	ENSCJAG00000007352	7 retrocopies	retro_cjac_1190, retro_cjac_1549, retro_cjac_161, retro_cjac_1878, retro_cjac_289, retro_cjac_4060, retro_cjac_679,
Cavia porcellus	ENSCPOG00000009017	2 retrocopies	retro_cpor_43, retro_cpor_550,
Macropus eugenii	ENSMEUG00000005744	2 retrocopies	retro_meug_1650, retro_meug_1973,
Macaca mulatta	ENSMMUG00000013395	1 retrocopy	retro_mmul_173,
Oryctolagus cuniculus	ENSOCUG00000016225	2 retrocopies	retro_ocun_346, retro_ocun_375,
Otolemur garnettii	ENSOGAG00000011713	3 retrocopies	retro_ogar_1847, retro_ogar_2767, retro_ogar_531,
Rattus norvegicus	ENSRNOG00000007235	5 retrocopies	retro_rnor_1342, retro_rnor_2240, retro_rnor_529, retro_rnor_64, retro_rnor_880,
Sus scrofa	ENSSSCG00000017544	1 retrocopy	retro_sscr_348,
Tursiops truncatus	ENSTTRG00000008526	1 retrocopy	retro_ttru_279 ,
Tursiops truncatus	ENSTTRG00000011524	3 retrocopies	retro_ttru_268, retro_ttru_510, retro_ttru_588,
Vicugna pacos	ENSVPAG00000007653	1 retrocopy	retro_vpac_282,