RetrogeneDB ID: retro_ttru_923

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_672:91147..91632(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C1orf43
• Ensembl ID: ENSTTRG00000015824
• Aliases: None
• Description: chromosome 1 open reading frame 43 [Source:HGNC Symbol;Acc:29876]

Sequence

>retro_ttru_923
TCTGGAGTGAATGTTGTGCTGGTAAAGGTCACGGGAATCTGGTATTTTTACTGCCATTTATTTTTGTGAAGAAGTAAATC
ATGAGCTTTGCAATGAAATCTTGAAGGGGACCTCATGTCCCCGAGGGGCACATGCCCCCAAAATCTTCAAACAGGAGACT
GATATTCTACTGTCCAGACTTTGGGATATCAAGTACAAACCTTGACTCCTTGTGGAGGATGGTCCAAGACTGCAACAGCT
GGAAACCCAAGGAAGTCAGAATTGCTACAACTATCTGCATAGGATGAAACTTATGGACACCATCTACGCCTCTGAAAACC
CACTTCGAGCTGAAGGCTGGCATCCCTATTCCTTAATGGGCAAGATTTTCGGCTCCTATCTGCTAGATCTTCCGAAACAC
TAGTAATCCTTTCAAGGGTGTCTGCAAGCCCTTCACCGATACCCTGCTGGATGGCTGAGACAGCCTGCCATGGGACATGG
GTCTG

Alignment

ORF - retro_ttru_923 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.06 %
• Parental protein coverage: 64.03 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SGVNVVLVMA-YGSLVFVLLFIFVKRQIMRFAMKSRRGPHVPVGH-NAPKDLKEEIDIRLSRVQDIKYEP
          SGVNVVLV....G.LVF.L.FIFVK..IM.FAMKS.RGPHVP.GH..APK..K.E.DI.LSR..DIKY.P
Retrocopy SGVNVVLVKV<HGNLVFLLPFIFVKK*IMSFAMKS*RGPHVPEGH<HAPKIFKQETDILLSRLWDIKYKP

Parental  QLLADDDARLLQLETQGNQNCYNYLYRMKALDAIRASEIPFHAEGRHPRSLMGKNFRSYLLDL-RNTSTP
          .LL..D..RL.QLETQG.QNCYNYL.RMK..D.I.ASE.P..AEG.HP.SLMGK.F.SYLLDL.RNTS.P
Retrocopy *LLVEDGPRLQQLETQGSQNCYNYLHRMKLMDTIYASENPLRAEGWHPYSLMGKIFGSYLLDL>RNTSNP

Parental  FKGVRKALIDTLLDGYETARYGTGV
          FKGV.K...DTLLDG........G.
Retrocopy FKGVCKPFTDTLLDG*DSLPWDMGL

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_923 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_923 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 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011865	1 retrocopy	retro_amel_190,
Callithrix jacchus	ENSCJAG00000009722	1 retrocopy	retro_cjac_175,
Dasypus novemcinctus	ENSDNOG00000019160	1 retrocopy	retro_dnov_2515,
Equus caballus	ENSECAG00000017585	2 retrocopies	retro_ecab_618, retro_ecab_814,
Echinops telfairi	ENSETEG00000001056	15 retrocopies	retro_etel_1138, retro_etel_1318, retro_etel_1388, retro_etel_1633, retro_etel_2182, retro_etel_2205, retro_etel_2206, retro_etel_394, retro_etel_651, retro_etel_719, retro_etel_720, retro_etel_773, retro_etel_842, retro_etel_957, retro_etel_981,
Macropus eugenii	ENSMEUG00000002600	6 retrocopies	retro_meug_1149, retro_meug_1298, retro_meug_1439, retro_meug_1637, retro_meug_213, retro_meug_69,
Myotis lucifugus	ENSMLUG00000013338	1 retrocopy	retro_mluc_537,
Monodelphis domestica	ENSMODG00000017237	3 retrocopies	retro_mdom_1283, retro_mdom_2003, retro_mdom_323,
Otolemur garnettii	ENSOGAG00000012008	2 retrocopies	retro_ogar_2563, retro_ogar_38,
Pteropus vampyrus	ENSPVAG00000002717	1 retrocopy	retro_pvam_696,
Rattus norvegicus	ENSRNOG00000017758	1 retrocopy	retro_rnor_139,
Sarcophilus harrisii	ENSSHAG00000012915	1 retrocopy	retro_shar_740,
Tursiops truncatus	ENSTTRG00000015824	1 retrocopy	retro_ttru_923 ,