RetrogeneDB ID: retro_ttru_1566

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_116422:104533..104839(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNRPD1
• Ensembl ID: ENSTTRG00000002654
• Aliases: None
• Description: small nuclear ribonucleoprotein D1 polypeptide 16kDa [Source:HGNC Symbol;Acc:11158]

Sequence

>retro_ttru_1566
CAGTTTTTGACGAAAATGAGTCACGACAGTGAAACCATTGAACTGAAGCATGGACACAGATGCATGAAATAATCATGGGG
GTAAATGTCAGCATGAGTACATGTCTCAAATCTCTGAGCGTGATCCTGAAAATCACAGAAACGGCACAGGGGGAGCACTG
AGAGTGCTGGGAATGGCATTTGATATGTTGTCCTGCCAGACAGTTTACCTCTGGGGACACTACTTGTGGACACTGAAACT
CAGGTGAAATCTCAGGAAAGGGAAGCCCTTGTCGGGAGAAACCGAGGCCAGGGAGGAGATGATGGG

Alignment

ORF - retro_ttru_1566 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.72 %
• Parental protein coverage: 89.57 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RFLMKLSHETVTIELKNG-TQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLE-TLSIRG-NNIRYFILP
          .FL.K.SH...TIELK.G.TQ.H..I.GV.VSM.T.LK.....LK..E..Q.E..L...G.N.I.Y..LP
Retrocopy QFLTKMSHDSETIELKHG<TQMHEIIMGVNVSMSTCLKSLSVILKITETAQGE<ALRVLG<NGI*YVVLP

Parental  DSLPLDTLLVDVEPKVKSKKREAVAGRGRGRGRGRG
          DSLPL.TLLVD.E..VKS..REA..GR.RG.G...G
Retrocopy DSLPLGTLLVDTETQVKSQEREALVGRNRGQGGDDG

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_1566 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1566 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 13 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000006364	1 retrocopy	retro_acar_129,
Bos taurus	ENSBTAG00000008292	3 retrocopies	retro_btau_144, retro_btau_706, retro_btau_84,
Canis familiaris	ENSCAFG00000018247	1 retrocopy	retro_cfam_373,
Dasypus novemcinctus	ENSDNOG00000018773	4 retrocopies	retro_dnov_1254, retro_dnov_1716, retro_dnov_1832, retro_dnov_2403,
Felis catus	ENSFCAG00000012352	1 retrocopy	retro_fcat_1885,
Macaca mulatta	ENSMMUG00000003992	2 retrocopies	retro_mmul_887, retro_mmul_891,
Mustela putorius furo	ENSMPUG00000005567	1 retrocopy	retro_mputfur_185,
Oryctolagus cuniculus	ENSOCUG00000023761	1 retrocopy	retro_ocun_224,
Pongo abelii	ENSPPYG00000025874	3 retrocopies	retro_pabe_254, retro_pabe_948, retro_pabe_952,
Pan troglodytes	ENSPTRG00000009909	2 retrocopies	retro_ptro_291, retro_ptro_781,
Pteropus vampyrus	ENSPVAG00000005511	1 retrocopy	retro_pvam_450,
Rattus norvegicus	ENSRNOG00000013714	2 retrocopies	retro_rnor_2671, retro_rnor_2729,
Tursiops truncatus	ENSTTRG00000002654	2 retrocopies	retro_ttru_1566 , retro_ttru_1890,