RetrogeneDB ID: retro_ttru_366

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_2012:171756..172699(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RIMKLB
• Ensembl ID: ENSTTRG00000000699
• Aliases: None
• Description: ribosomal modification protein rimK-like family member B [Source:HGNC Symbol;Acc:29228]

Sequence

>retro_ttru_366
ATGTGTAGCTCTGTGGCTGCCAAGTTGTGGTTTTTGACAGATCGTCAAATCAGAGAAGACTATCCCCCAAAAGAGATCTT
ACGAGCATTAAAGGCCAAATGTTGTGAGGAGGAACTGGACTTTAGGGCTGTGGTGATAGATGAGGTGGTGCTAACAATCG
AGCAAGGAAACCTGGGTCTTTGTATCGATGGAGAACTAATTACTGCCTGTCCTCAGGTGGTGGTAGTGACAGTACCAACC
CCTTGGGTGCAAAGTGATAGTGACGTCACTGTTTTGCGCCATCTAGAGAAGGTGGGAAGCAGGTTGATGAACTGACCTCA
AACCGTCCTGAACTGTGTTAATAAGTCTTGGATGTTTCAAGAGTTGGCAGGTCATGGTGTTCCTCTGCCAGACACTTTCT
CTTACGGTGGTCATGAAAATTTTGCTAAAATGACTGATGAAGCAGAAGTACTGGAGTTCCCAAAGGTGGTGAAGAATACA
CGGGGTCATAGAGGCAAAGCAGTTTTCTTGGCTCGCGATAAGCACCCTTTGGCTAATCTAAGCCATCTTATTCGCCATGA
AGCTCCATACCTATTTCAGAAGTATGTTAAAGAGTCTCATGGAAGGGATGTACGTGTCATTGTCGTGGGATGTCGTGTGG
TTGGCACAATGTTACGCTGTTCAACAGATGGGAGGATGCAAAGAAACTGCTCACTAGGTGGTGTCGGGATGATGTGCTCA
TTGAGTTAACAAGGGAAGCAGCTAGCTATGCAGGTGTCTAACATCCTGGGATCGGATGTGTGTAGCACTGACCTGTTGAT
GAAAGACGACAGCTCCTTCTGTGTCTGCGAGGCCAATGCAAATGTAGTTTCATTGCCTTTGATAAGCGTGTTATCTAGAT
GTAGCTGGTATCATAGCGGACTATGCCGCCTCCCTTCTGCCCTCTGGCCGCCTCACCCGGCGT

Alignment

ORF - retro_ttru_366 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.59 %
• Parental protein coverage: 81.61 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MCSSVAAKLWFLTDRRIREDYPQKEILRALKAKCCEEELDFRAVVMDEVVLTVEQGNLGLRINGELITAY
          MCSSVAAKLWFLTDR.IREDYP.KEILRALKAKCCEEELDFRAVV.DEVVLT.EQGNLGL.I.GELITA.
Retrocopy MCSSVAAKLWFLTDRQIREDYPPKEILRALKAKCCEEELDFRAVVIDEVVLTIEQGNLGLCIDGELITAC

Parental  PQVVVVRVPTPWVQSDSDITVLRHLEKMGCRLMNRPQAILNCVNKFWTFQELAGHGVPLPDTFSYGGHEN
          PQVVVV.VPTPWVQSDSD.TVLRHLEK.G.RLMN.PQ..LNCVNK.W.FQELAGHGVPLPDTFSYGGHEN
Retrocopy PQVVVVTVPTPWVQSDSDVTVLRHLEKVGSRLMN*PQTVLNCVNKSWMFQELAGHGVPLPDTFSYGGHEN

Parental  FAKMIDEAEVLEFPMVVKNTRGHRGKAVFLARDKHHLADLSHLIRHEAPYLFQKYVKESHGRDVRVIVVG
          FAKM.DEAEVLEFP.VVKNTRGHRGKAVFLARDKH.LA.LSHLIRHEAPYLFQKYVKESHGRDVRVIVVG
Retrocopy FAKMTDEAEVLEFPKVVKNTRGHRGKAVFLARDKHPLANLSHLIRHEAPYLFQKYVKESHGRDVRVIVVG

Parental  GRVVGTMLRCSTDGRMQSNCSLGGVGMMCSLSEQGKQLAIQVSNILGMDVCGIDLLTKDDGSFCVCEANA
          .RVVGTMLRCSTDGRMQ.NCSLGGVGMMCSLS.QGKQLA.QVSNILG.DVC..DLL.KDD.SFCVCEANA
Retrocopy CRVVGTMLRCSTDGRMQRNCSLGGVGMMCSLS*QGKQLAMQVSNILGSDVCSTDLLMKDDSSFCVCEANA

Parental  NV-GFIAFDK-ACNLDVAGIIADYAASLLPSGRLTRR
          NV..FIAFDK.AC.LDVAGIIADYAASLLPSGRLTRR
Retrocopy NV<SFIAFDK<ACYLDVAGIIADYAASLLPSGRLTRR

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_366 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_366 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
Gorilla gorilla	ENSGGOG00000000332	1 retrocopy	retro_ggor_31,
Rattus norvegicus	ENSRNOG00000023814	1 retrocopy	retro_rnor_255,
Tursiops truncatus	ENSTTRG00000000699	3 retrocopies	retro_ttru_1672, retro_ttru_366 , retro_ttru_460,
Vicugna pacos	ENSVPAG00000003954	1 retrocopy	retro_vpac_256,