RetrogeneDB ID: retro_ttru_1908

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_98308:1821..2163(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL30
• Ensembl ID: ENSTTRG00000016058
• Aliases: None
• Description: ribosomal protein L30 [Source:HGNC Symbol;Acc:10333]

Sequence

>retro_ttru_1908
ATGGTGGCTGCAAAGAAGAAGAAAAAGTCACTGGAGTCAATCAACTCTGGGTTCCAACTCGTTATGAAAAGTGGAAAGTA
TGTGCTGGGGTACAAGCTGACTTTGAAAATGATCAGACAAGGCAAAGCGAAACTGGTCATCCTCGCCAACTGCCCAGCCT
TGAAGAAATCTGAAATAGAGTATTATGCCATGTTGGCCAAAACTGGTGTTCATCACTACAGTGGTAATAATATTGAATTG
GGCAGAGTGTGTGGAAAATACTACAGAGGATACACAATGGCTATCACTGATCCAGGTGATTCTGATATTATTAAAAGCAT
GCCCGCACAGACTAGTGAAAGG

Alignment

ORF - retro_ttru_1908 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.22 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVAAKKTKKSLESINSRLQLVMKSGKYVLGYKQTLKMIRHGKAKLVILANNCPALRKSEIEYYAMLAKTG
          MVAAKK.KKSLESINS..QLVMKSGKYVLGYK.TLKMIR.GKAKLVILAN.CPAL.KSEIEYYAMLAKTG
Retrocopy MVAAKKKKKSLESINSGFQLVMKSGKYVLGYKLTLKMIRQGKAKLVILAN-CPALKKSEIEYYAMLAKTG

Parental  VHHYSGNNIELGTACGKYYRVCTLAIIDPGDSDIIRSMPEQTGEK
          VHHYSGNNIELG..CGKYYR..T.AI.DPGDSDII.SMP.QT.E.
Retrocopy VHHYSGNNIELGRVCGKYYRGYTMAITDPGDSDIIKSMPAQTSER

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_1908 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1908 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 10 parental genes, and 61 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000016047	2 retrocopies	retro_acar_170, retro_acar_47,
Ailuropoda melanoleuca	ENSAMEG00000000605	18 retrocopies	retro_amel_1007, retro_amel_1148, retro_amel_1205, retro_amel_1456, retro_amel_1490, retro_amel_1596, retro_amel_1709, retro_amel_1738, retro_amel_26, retro_amel_384, retro_amel_40, retro_amel_456, retro_amel_50, retro_amel_534, retro_amel_551, retro_amel_642, retro_amel_745, retro_amel_806,
Bos taurus	ENSBTAG00000016278	2 retrocopies	retro_btau_34, retro_btau_992,
Callithrix jacchus	ENSCJAG00000015549	4 retrocopies	retro_cjac_14, retro_cjac_253, retro_cjac_320, retro_cjac_351,
Felis catus	ENSFCAG00000002165	9 retrocopies	retro_fcat_1261, retro_fcat_1391, retro_fcat_1473, retro_fcat_1689, retro_fcat_1872, retro_fcat_323, retro_fcat_45, retro_fcat_49, retro_fcat_754,
Loxodonta africana	ENSLAFG00000002077	2 retrocopies	retro_lafr_122, retro_lafr_882,
Microcebus murinus	ENSMICG00000004620	3 retrocopies	retro_mmur_258, retro_mmur_644, retro_mmur_693,
Macaca mulatta	ENSMMUG00000020073	12 retrocopies	retro_mmul_1353, retro_mmul_2275, retro_mmul_2291, retro_mmul_2309, retro_mmul_2322, retro_mmul_2473, retro_mmul_29, retro_mmul_319, retro_mmul_416, retro_mmul_576, retro_mmul_663, retro_mmul_857,
Oryctolagus cuniculus	ENSOCUG00000017386	4 retrocopies	retro_ocun_1447, retro_ocun_1580, retro_ocun_178, retro_ocun_279,
Tursiops truncatus	ENSTTRG00000016058	5 retrocopies	retro_ttru_167, retro_ttru_1871, retro_ttru_1908 , retro_ttru_1941, retro_ttru_509,