RetrogeneDB ID: retro_ttru_1672

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_84832:2409..3264(-)
• 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_1672
ATGTGTAGCTCTGTGGCCGCCAAGTTGTGGTTTTTGACAGATCGTCGAATCAGGGAAGACTACCCTCAAAAAGAGATCTT
ACGAGCGTTCAAGGCCAAATGTTGTGAGGAGGAACTGGACTTTAGGGCTGTGGTGATGGATGAGGTGGTGCTGACAGCTG
AGCAAGGAAACCTGGGTCTTCGTATGAAAGGAGAACTAATTACTGCTTACCCTCAGGTGGTGGTAGTGAGAGTACCAACC
CCTTGGGTGCAAAGTGATAGTGACATCACTGTTTTGCGCCATCTAGAGAAGATGGGATGCAGGTGGATGAACCGACCTCA
AGCCATCCTGAACTGTGGTAATAAGTTCTGGACGTTTCAAGAGTTGGCAGGTCATGGTATTCCTCTGCCAGATACCTTCT
CTTATGGTGGTCATGAAAATTTTGCTAACATGATTGATGAAGCTGAAGTACTGGAGTTCCCAATGGTGGTGAGGAATACA
CGGGGCCATAGAGGCAAAGCAGTTTTCTTGGCTCGCGATAAGCACCATTTGGCTGATCTAAGCCATCTTATTCGCCATGA
AGCTCCATACCTGTTTCAGAAGTGTGTTAAAGAGTCTCACGGAAGGGATGTACGTGTCATTGTTGTGGGACGCCGTGCGG
TTGGCACCATGTTACGCTGTTCAACAGATGGGAGGATGCAAAGCAACTGCTCACTGGGTGGTATACGGATGATGTGCTCA
TTGAGTGAACACGGGAAACAGCTAGCTATCCAGGTGTCTAACATCCTGGGAATGAATGTGTGTGGCATTGACCTGTTGAT
GAAAGACAACGGCTCCTTCTGTGTCTGCGAGGCCAGTGCAAATGTAGGTTTGATA

Alignment

ORF - retro_ttru_1672 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.98 %
• Parental protein coverage: 73.83 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MCSSVAAKLWFLTDRRIREDYPQKEILRALKAKCCEEELDFRAVVMDEVVLTVEQGNLGLRINGELITAY
          MCSSVAAKLWFLTDRRIREDYPQKEILRA.KAKCCEEELDFRAVVMDEVVLT.EQGNLGLR..GELITAY
Retrocopy MCSSVAAKLWFLTDRRIREDYPQKEILRAFKAKCCEEELDFRAVVMDEVVLTAEQGNLGLRMKGELITAY

Parental  PQVVVVRVPTPWVQSDSDITVLRHLEKMGCRLMNRPQAILNCVNKFWTFQELAGHGVPLPDTFSYGGHEN
          PQVVVVRVPTPWVQSDSDITVLRHLEKMGCR.MNRPQAILNC.NKFWTFQELAGHG.PLPDTFSYGGHEN
Retrocopy PQVVVVRVPTPWVQSDSDITVLRHLEKMGCRWMNRPQAILNCGNKFWTFQELAGHGIPLPDTFSYGGHEN

Parental  FAKMIDEAEVLEFPMVVKNTRGHRGKAVFLARDKHHLADLSHLIRHEAPYLFQKYVKESHGRDVRVIVVG
          FA.MIDEAEVLEFPMVV.NTRGHRGKAVFLARDKHHLADLSHLIRHEAPYLFQK.VKESHGRDVRVIVVG
Retrocopy FANMIDEAEVLEFPMVVRNTRGHRGKAVFLARDKHHLADLSHLIRHEAPYLFQKCVKESHGRDVRVIVVG

Parental  GRVVGTMLRCSTDGRMQSNCSLGGVGMMCSLSEQGKQLAIQVSNILGMDVCGIDLLTKDDGSFCVCEANA
          .R.VGTMLRCSTDGRMQSNCSLGG..MMCSLSE.GKQLAIQVSNILGM.VCGIDLL.KD.GSFCVCEA.A
Retrocopy RRAVGTMLRCSTDGRMQSNCSLGGIRMMCSLSEHGKQLAIQVSNILGMNVCGIDLLMKDNGSFCVCEASA

Parental  NVGFI
          NVG.I
Retrocopy NVGLI

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_1672 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1672 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,