RetrogeneDB ID: retro_ttru_918

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_646:41846..42732(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CYB5R3
• Ensembl ID: ENSTTRG00000015143
• Aliases: None
• Description: cytochrome b5 reductase 3 [Source:HGNC Symbol;Acc:2873]

Sequence

>retro_ttru_918
TTGGGCCACGTGGTCCTCTCCCCAGTCTGGTTCCTGTACAGCCTGCTCATGAAGCTGTTCCAAAGCTCCACTCCCGCCAT
CACCCTCGAGAACCTGGACATCAAGTACCTGCTGCGGCTGATTGACAAGGAGGTCATCAGCCTTGACACCTGATGGTTCC
ACTTTGCTCTACCGTCGCCCCAGCACATCCTGGGCCTCCCCGTAGGGCTAGCACATCTACCTCTCGGCTTGAATCAATGG
GAACCTGGTCATTCTGCCCTACATGCCTGTCTCCAGCGATGACAAGGGCTTTGTGGACCTGGTCATCAAGGTTTACTTCA
AAGACACTCACCCCAAGTTTCCCGCTGGTGGGATGTCCCAGATGTCCCAGTACCTGTAAAGCATGAAGATTGGAGGCACC
ATTGAGTTCCGAGACCCAAATGGGCTGCCGGTCTACCAGGGCAAAGGAAAGTTTGCCATCTGTGCAGACAAGAAATCCAA
CCCTGTCATCAAGACGGTGAAGTCTGTGGGCATGTTTGCGGGAGGAACGGGCATCACCCCAATGCTATAGGTGATCCGCG
CCATCATGAAGGACAGGGATGATCACACCATGTGCCACCTGCGCTTTGCCAACCAGACTGAGAAGGACCTCCTGCTGCGG
CTGGAGCTGGAGGAACTGAAGAACGAACATTCTGAGTGCTTCAAGCTCTGGTACATGGTGGACAGTGCCCCTGAAGCTTG
GGACTACAGCCAGGGCTTCGTGAACGAGGAGATGATCTGGGACCACCTTCCACCCCTGGAGGAGGAGCCACTGGTGCTGA
TGTGCGGACCCCCGTGCATGATCCAGTATGCCTACCTGCCCAATCTGGACAGCGTGGGCCACCCCAAGGAGCGCTCCTTC
GCCTTC

Alignment

ORF - retro_ttru_918 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.51 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LGHVVLSPVWFLYSLFMKLFQRSTPAITLENPDIKYPLRLIDKEVISHDTRRFRFALPSPQHILGLPVGQ
          LGHVVLSPVWFLYSL.MKLFQ.STPAITLEN.DIKY.LRLIDKEVIS.DT..F.FALPSPQHILGLPVG.
Retrocopy LGHVVLSPVWFLYSLLMKLFQSSTPAITLENLDIKYLLRLIDKEVISLDT*WFHFALPSPQHILGLPVGL

Parental  -HIYLSARIDGNLVIRPYTPVSSDDDKGFVDLVIKVYFKDTHPKFPAGG--KMSQYLESMKIGDTIEFRG
          .HIYLSA.I.GNLVI.PY.PVSSDD.KGFVDLVIKVYFKDTHPKFPAGG...MSQYL.SMKIG.TIEFR.
Retrocopy >HIYLSA*INGNLVILPYMPVSSDD-KGFVDLVIKVYFKDTHPKFPAGGMSQMSQYL*SMKIGGTIEFRD

Parental  PNGLLVYQGKGTFAIRPDKKSSPVITTVKSVGMIAGGTGITPMLQVIRAIMKDPDDQTVCHLLFANQTEK
          PNGL.VYQGKG.FAI..DKKS.PVI.TVKSVGM.AGGTGITPML.VIRAIMKD.DD.T.CHL.FANQTEK
Retrocopy PNGLPVYQGKGKFAICADKKSNPVIKTVKSVGMFAGGTGITPML*VIRAIMKDRDDHTMCHLRFANQTEK

Parental  DILLRPELEELRNEHSARFKLWYTVDKAPEAWDYSQGFVNEEMIRDHLPPPEEEPLVLMCGPPPMIQYAC
          D.LLR.ELEEL.NEHS..FKLWY.VD.APEAWDYSQGFVNEEMI.DHLPP.EEEPLVLMCGPP.MIQYA.
Retrocopy DLLLRLELEELKNEHSECFKLWYMVDSAPEAWDYSQGFVNEEMIWDHLPPLEEEPLVLMCGPPCMIQYAY

Parental  LPNLDRVGHPKERCFAF
          LPNLD.VGHPKER.FAF
Retrocopy LPNLDSVGHPKERSFAF

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_918 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_918 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 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009549	1 retrocopy	retro_amel_1305,
Bos taurus	ENSBTAG00000016516	2 retrocopies	retro_btau_1244, retro_btau_1287,
Pteropus vampyrus	ENSPVAG00000014126	1 retrocopy	retro_pvam_310,
Tursiops truncatus	ENSTTRG00000015143	2 retrocopies	retro_ttru_408, retro_ttru_918 ,