RetrogeneDB ID: retro_ttru_1777

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_91267:45414..45900(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDLIM1
• Ensembl ID: ENSTTRG00000012118
• Aliases: None
• Description: PDZ and LIM domain 1 [Source:HGNC Symbol;Acc:2067]

Sequence

>retro_ttru_1777
GTCACTCCCAGAAGCAAGGCTGCTATAGCTAATTCTGTGTGTAATCACAGCCATTGATGGGGAAAATACCAGCAATATGA
TGCACTTGGAAGCTCAGAACAAAATCAAGGGCTGCACAGACAATGTGACTCTCATAGTAGCCAGATCTGAAAGAAAATAT
GGTCTCCTCTGGTGACAGAGGAAGGGAAACATCACTCATATAAGATGAATTTAGTCTCTGAACCCCAAGAGGTCCTACAT
ATAGGAAGCGCCCACAACAAAAGTTCCATGCCCTTTACCATCTCACCTGCCTCCAGTTCTACCCCCAGGGTCATCACAAA
CCAGTACAACAACCCAGCTGACTTCTACTCTTCTGAAAACATCTCCAACTTCAACTATGCCTTGGAGTCAAAGAAAGCAG
CCAGTGGGCAGGAGATGAATGGCAGAGCCTTAGACCATTCTCAGCTTCCAAGCAGACTTGTCATTGACAAAGATTCTGAA
GTCTTC

Alignment

ORF - retro_ttru_1777 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.23 %
• Parental protein coverage: 84.18 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VTPGSKAATAN-LCVGDVITAIDGENTSNMTHLEAQNKIKGCTDNMTLTVTRSEQK-IWSPLVTEEGKRH
          VTP.SKAA.AN.LC...VITAIDGENTSNM.HLEAQNKIKGCTDN.TL.V.RSE.K.IWSPLVTEEGK.H
Retrocopy VTPRSKAAIAN>LC---VITAIDGENTSNMMHLEAQNKIKGCTDNVTLIVARSERK<IWSPLVTEEGKHH

Parental  PYKMNLASEPQEVLHIGSAHNRSAMPFTASPASSPAPRVITNQYNNPAGLYSPENISNFNNALESKTAAS
          .YKMNL.SEPQEVLHIGSAHN.S.MPFT.SPASS..PRVITNQYNNPA..YS.ENISNFN.ALESK.AAS
Retrocopy SYKMNLVSEPQEVLHIGSAHNKSSMPFTISPASSSTPRVITNQYNNPADFYSSENISNFNYALESKKAAS

Parental  GQEMNGRALDHSQLPSGLVIDKESEVY
          GQEMNGRALDHSQLPS.LVIDK.SEV.
Retrocopy GQEMNGRALDHSQLPSRLVIDKDSEVF

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_1777 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1777 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.

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011182	1 retrocopy	retro_btau_690,
Canis familiaris	ENSCAFG00000028553	1 retrocopy	retro_cfam_2080,
Dasypus novemcinctus	ENSDNOG00000012381	1 retrocopy	retro_dnov_1119,
Homo sapiens	ENSG00000107438	2 retrocopies	retro_hsap_1815, retro_hsap_2681,
Macaca mulatta	ENSMMUG00000000454	2 retrocopies	retro_mmul_1250, retro_mmul_1419,
Mus musculus	ENSMUSG00000055044	2 retrocopies	retro_mmus_2558, retro_mmus_779,
Nomascus leucogenys	ENSNLEG00000013055	3 retrocopies	retro_nleu_1819, retro_nleu_2767, retro_nleu_2970,
Oryctolagus cuniculus	ENSOCUG00000013643	1 retrocopy	retro_ocun_417,
Pongo abelii	ENSPPYG00000002507	2 retrocopies	retro_pabe_1109, retro_pabe_1485,
Pan troglodytes	ENSPTRG00000002783	1 retrocopy	retro_ptro_912,
Tarsius syrichta	ENSTSYG00000000834	2 retrocopies	retro_tsyr_1056, retro_tsyr_1224,
Tursiops truncatus	ENSTTRG00000012118	2 retrocopies	retro_ttru_1777 , retro_ttru_976,