RetrogeneDB ID: retro_ttru_159

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_1431:400038..400993(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP5A1
• Ensembl ID: ENSTTRG00000005118
• Aliases: None
• Description: ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1, cardiac muscle [Source:HGNC Symbol;Acc:823]

Sequence

>retro_ttru_159
ATGCTGTCTGGACACGTGGCCTTGGGCTGTGGCTTGCACCCTCCCTTGGCAGGCCAGACTGGTCTTCAGAATGCTTTGGG
ATCATCCTTCATTGCCACAGGGAACCTCCATGCCTCTTAACACTTGTCTTCAGACGACTGGCACTGCTGAGGTATCCTCT
GTTCTTGAAGAGCGTAATCTTGGAGCCAAAACCTCTGTTGACTGTGAAGAAACAGGTGTGTCTCAAGTATTGATGATAGT
ATTGGTTGAATACATGGGCTGAGGAATGTTCAAGCAGACGAAATGGTAGTGTTTTCTTCAGGCTTAAAGGGTATGTTTCA
ACTTGGGAACTGACAATGTTGGTTTTGTTGTGTTTGGACATGATAAACTAATTAAGGAAGGAGATACTGTGAAGAGGACG
GGAGCCATTGTGAATGTTCTAGTTGGTGAGAAGCTACTGGGTTGTATAGTAGATGCCCTTGGTAATGTCACTGATGAAAA
GGATCCAGTTGGTTCCAAGACCCAATGGTGAGTTGGCCTGAAAGCCCCTGGCATCATTTCTCCAATCTCTGTGCAGAAAC
CAGTGCAGACTGGCATTAATGCTGTGGATAGCTTGGCACTGATTGGTTGTGGTCAGTACAGGCTGACGATTGGTGACTGA
CAGACTGGCAGAACATCAATGATTGACATAATTATTAACCAGAAACATTTCAGTGATGGATCTGATGGAAAGAAGCAGCT
ATACTATATCTACACTGCTATCGGTCAGAAGAGATCCACTGTTGCCCAGTTGGTGAAAACACTTACAGATGTGGATGCCA
TGAAGAACACCAGTGTGGTTTCAACCACTGCTGCTGACACTGCCCTCCATCAGTACCTGACTCCTTATTCTTGCTGTGCT
GTGGGAGAGCATTTTAGGGATAATGGCAAACATGCTTTGATCATCTGTGATGAATTATCCAAGCAGGCTGGTGCC

Alignment

ORF - retro_ttru_159 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.87 %
• Parental protein coverage: 57.79 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MLSVRVAA-AVARALPRRAGLVSK-NALGSSFIAVRNLHAS-NSRLQKTGTAEVSSILEERILGADTSVD
          MLS..VA..AVA..LP..A.LV...NALGSSFIA..NLHAS.N..LQ.TGTAEVSS.LEER.LGA.TSVD
Retrocopy MLSGHVAL>AVACTLPWQARLVFR<NALGSSFIATGNLHAS>NTCLQTTGTAEVSSVLEERNLGAKTSVD

Parental  LEETGR-VLSIGDGIARVHGLRNVQAEEMVEFSSGL-KG-MSLNLEPDNVGVVVFGNDKLIKEGDIVKRT
          .EETG..V.SI.D.I...HGLRNVQA.EMV.FSSGL.KG....NL..DNVG.VVFG.DKLIKEGD.VKRT
Retrocopy CEETGV<VSSIDDSIG*IHGLRNVQADEMVVFSSGL<KG<VCFNLGTDNVGFVVFGHDKLIKEGDTVKRT

Parental  GAIVDVPVGEELLGRVVDALGNAIDGKGPIGSKTRRRVGLKAPGIIPRISVREPMQTGIKAVDSLVPIGR
          GAIV.V.VGE.LLG..VDALGN..D.K.P.GSKT...VGLKAPGII..ISV..P.QTGI.AVDSL..IG.
Retrocopy GAIVNVLVGEKLLGCIVDALGNVTDEKDPVGSKTQW*VGLKAPGIISPISVQKPVQTGINAVDSLALIGC

Parental  GQRELIIGDRQTGKTSIAIDTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDAXXXXXXXX
          GQ..L.IGD.QTG.TS..ID.IINQK.F.DG.D.KK.LY.IY.AIGQKRSTVAQLVK.LTD.........
Retrocopy GQYRLTIGD*QTGRTSM-IDIIINQKHFSDGSDGKKQLYYIYTAIGQKRSTVAQLVKTLTDVDAMKNTSV

Parental  XXXXXSDAAPLQYLA-YSGCFMREYFRDNGKHALIIYDDLSKQAVA
          ......D.A..QYL..YS.C...E.FRDNGKHALII.D.LSKQA.A
Retrocopy VSTTAADTALHQYLTPYSCCAVGEHFRDNGKHALIICDELSKQAGA

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_159 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_159 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 18 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002507	2 retrocopies	retro_btau_1380, retro_btau_1426,
Canis familiaris	ENSCAFG00000017648	2 retrocopies	retro_cfam_1483, retro_cfam_516,
Dasypus novemcinctus	ENSDNOG00000006331	2 retrocopies	retro_dnov_1740, retro_dnov_2525,
Equus caballus	ENSECAG00000021561	1 retrocopy	retro_ecab_788,
Homo sapiens	ENSG00000152234	1 retrocopy	retro_hsap_1702,
Gorilla gorilla	ENSGGOG00000016560	1 retrocopy	retro_ggor_1275,
Meleagris gallopavo	ENSMGAG00000009963	1 retrocopy	retro_mgal_14,
Microcebus murinus	ENSMICG00000017500	1 retrocopy	retro_mmur_1210,
Myotis lucifugus	ENSMLUG00000009856	1 retrocopy	retro_mluc_1198,
Macaca mulatta	ENSMMUG00000003570	1 retrocopy	retro_mmul_1208,
Mustela putorius furo	ENSMPUG00000000923	1 retrocopy	retro_mputfur_601,
Nomascus leucogenys	ENSNLEG00000010973	1 retrocopy	retro_nleu_1334,
Oryctolagus cuniculus	ENSOCUG00000003967	1 retrocopy	retro_ocun_1235,
Pongo abelii	ENSPPYG00000009130	1 retrocopy	retro_pabe_1363,
Pan troglodytes	ENSPTRG00000009991	1 retrocopy	retro_ptro_1151,
Sarcophilus harrisii	ENSSHAG00000017177	1 retrocopy	retro_shar_109,
Tarsius syrichta	ENSTSYG00000007804	1 retrocopy	retro_tsyr_1186,
Tursiops truncatus	ENSTTRG00000005118	1 retrocopy	retro_ttru_159 ,