RetrogeneDB ID: retro_ttru_30

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_1799:1156925..1157930(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTTRG00000016156
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: FBL
• Ensembl ID: ENSTTRG00000003967
• Aliases: None
• Description: fibrillarin [Source:HGNC Symbol;Acc:3599]

Sequence

>retro_ttru_30
ATGAAGTCGGCGGTGAGCGCGCGCGGTGGGGTGTCTGGCGGCCGCGGAGGTGGCTGCTGGGGCGGGGGGCGAGGAGGCGG
AGGAGGAGGCGGGGGCAAAGGAGGAGGCGGGGGCAAAGGACCGGGAGGCGATGGCGGCGGCCAGGGGGGCAAGGGCGGCT
TCGGAGCGCGGACGCGCGGCTTCGGAGGCGGCAGGGGCAGGGGGCGCGGTGGTGGAGACGGCAGGGACCGCGGAGGCGGC
GGGCAGCGGCGTGGCGTGGCCAAGAGCAAGAACCGCCGCAGGAAGGGCGTCACCACGGTATCCGTGGAACCGCACCGGCA
CGAGGGGGTCTTTATCTACCGCGGGGCGGAGGACGCTCTGGTCACACTGAATATGGTGCCCGGCCAGTCGGTGTACGGCG
AGCGGCGGGTCACGGTGACCGAGGGCGGCGTGAAACAGGAGTACCGCACGTGGAACCCCTTCCGTTTCAAGCTGGCCGCG
GCCATACTGGGCGGGGTCGACCAGATTCACATCAAGCCCAAGTCCAAAGTGCTCTACCTGGGTGCCGCCTCGGGGACCAC
CGTCTCCCACGTCTCCGACATCATCGGCCCTGATGGCCTAGTCTACGCGGTCGAGTTCTCCCACCGCGCCGGCCGCGATC
TGGTCAACGTGGCCAAGAAGAGAACCAACATCATCCCAGTCCTCGAAGACGCCCGGCACCCCCTCAAGTACCGCATGCTC
ATCGGGATGGTGGACGTGATCTTTGCCGACGTGGCCCAGCCAGACCAGTCCCGCATCGTGGCTCTGAATGCCCACACCTT
CCTGCGCAACGGGGGCCACTTCCTCATTTCCATCAAGGCCAATTGCATCGACTCCACCGCCTCTGCTGAGGCGGTGTTTG
CTTCTGAGGTGAGGAAGTTGCAGCAGGAGAATTTGAAGCCTCAAGAGCAGCTGACCCTGGAGCCCTATGAGAGGGACCAC
GCTGTGGTCGTCGGGGTCTATCGGCCCCTTCCCAAGAGCGCCAAC

Alignment

ORF - retro_ttru_30 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.08 %
• Parental protein coverage: 97.83 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RGGGF--SGRGGFGDRGGRGGGRGGFGGGRGGFGGGRGGFGEGRGRGGGFRGRGRGGGGGGFQSGGSRGR
          RGGG....GRGG.G..GG.GGG.G...GG.GG..GG.GGFG......GG.RGRGRGGG.G....GG...R
Retrocopy RGGGCWGGGRGGGGGGGGKGGGGGKGPGGDGGGQGGKGGFGARTRGFGGGRGRGRGGGDGRDRGGGGQRR

Parental  G--RGGRKGNQSGKNVMVEPHRHEGVFICRGKEDALVTKNLVPGESVYGEKRVSISEGDDKIEYRAWNPF
          G..............V.VEPHRHEGVFI.RG.EDALVT.N.VPG.SVYGE.RV...EG..K.EYR.WNPF
Retrocopy GVAKSKNRRRKGVTTVSVEPHRHEGVFIYRGAEDALVTLNMVPGQSVYGERRVTVTEGGVKQEYRTWNPF

Parental  RSKLAAAILGGVDQIHIKPGAKVLYLGAASGTTVSHVSDIVGPDGLVYAVEFSHRSGRDLINLAKKRTNI
          R.KLAAAILGGVDQIHIKP..KVLYLGAASGTTVSHVSDI.GPDGLVYAVEFSHR.GRDL.N.AKKRTNI
Retrocopy RFKLAAAILGGVDQIHIKPKSKVLYLGAASGTTVSHVSDIIGPDGLVYAVEFSHRAGRDLVNVAKKRTNI

Parental  IPVIEDARHPHKYRMLIAMVDVI-ADVAQPDQTRIVAVNAHTFVRNGGHFVISIKANCIDSTASAEAVFA
          IPV.EDARHP.KYRMLI.MVDVI.ADVAQPDQ.RIVA.NAHTF.RNGGHF.ISIKANCIDSTASAEAVFA
Retrocopy IPVLEDARHPLKYRMLIGMVDVIFADVAQPDQSRIVALNAHTFLRNGGHFLISIKANCIDSTASAEAVFA

Parental  SEVKKMQQENMKPQEQLTLEPYERDHAVVVGVYRPPPKVKN
          SEV.K.QQEN.KPQEQLTLEPYERDHAVVVGVYRP.PK..N
Retrocopy SEVRKLQQENLKPQEQLTLEPYERDHAVVVGVYRPLPKSAN

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_30 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_30 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 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000023221	1 retrocopy	retro_ecab_308,
Loxodonta africana	ENSLAFG00000000171	1 retrocopy	retro_lafr_23,
Macropus eugenii	ENSMEUG00000014684	1 retrocopy	retro_meug_1077,
Rattus norvegicus	ENSRNOG00000019229	4 retrocopies	retro_rnor_1082, retro_rnor_1780, retro_rnor_643, retro_rnor_75,
Sorex araneus	ENSSARG00000008709	1 retrocopy	retro_sara_768,
Ictidomys tridecemlineatus	ENSSTOG00000012486	1 retrocopy	retro_itri_1302,
Tursiops truncatus	ENSTTRG00000003967	1 retrocopy	retro_ttru_30 ,