RetrogeneDB ID: retro_ttru_85

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_1180:88044..88485(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NPC2
• Ensembl ID: ENSTTRG00000013025
• Aliases: None
• Description: Niemann-Pick disease, type C2 [Source:HGNC Symbol;Acc:14537]

Sequence

>retro_ttru_85
ATGCGTTTCTTGGGCGCCGCGTTCCTGTTCCTGGCACTCAGCGCCTCTGCCCTGGCCAAGCCGGTGCATTTCAAGGACTG
CGGTTCTGGGGTCGGAGTTATAAAGGAGGTGAATGTGAATCCATACTCCACCCAGCCCTGCCAACTGCACAAAGGACAGT
CTTACAGTGTCAATGTCACGTTCACCAGTAGCACTCAGTCTCAAAGTAGCAAAGCCATGGTGCGTGGCATTGTGATGGGT
TTCGCCATTCCCTTTCCTATTCCTGAGCTTGACGGTTGTAAGAGTGGAATCAGCTGCCCCATTGAAAAAGACAAGACCTA
TAGCTACTTGAATAAACTACCTGTGAAGAGTGAATACCCCTCTGTAAAACTGGTGGTGGAGTGGGAACTTACGGATGACA
ACGACCAACGTCTCTTCTGCTGGCAAATCCCAGTACAGATT

Alignment

ORF - retro_ttru_85 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.88 %
• Parental protein coverage: 96.69 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRFLGAAFLFLALSASALAEPVHFKDCGSGVGVIKEVNVNPCSTE-CQLHKGQSYSVNVTFTSSTQSQSS
          MRFLGAAFLFLALSASALA.PVHFKDCGSGVGVIKEVNVNP.ST..CQLHKGQSYSVNVTFTSSTQSQSS
Retrocopy MRFLGAAFLFLALSASALAKPVHFKDCGSGVGVIKEVNVNPYSTQPCQLHKGQSYSVNVTFTSSTQSQSS

Parental  KAVVHGIVMGVAIPFPIPEPDGCKSGISCPIEKDKTYSYLNKLPVKSEYPSIKLVVEWELTDDNDQRLFC
          KA.V.GIVMG.AIPFPIPE.DGCKSGISCPIEKDKTYSYLNKLPVKSEYPS.KLVVEWELTDDNDQRLFC
Retrocopy KAMVRGIVMGFAIPFPIPELDGCKSGISCPIEKDKTYSYLNKLPVKSEYPSVKLVVEWELTDDNDQRLFC

Parental  WQIPVQI
          WQIPVQI
Retrocopy WQIPVQI

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_85 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_85 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000016932	1 retrocopy	retro_cfam_2050,
Choloepus hoffmanni	ENSCHOG00000009488	1 retrocopy	retro_chof_2335,
Echinops telfairi	ENSETEG00000003719	2 retrocopies	retro_etel_1610, retro_etel_1866,
Loxodonta africana	ENSLAFG00000002876	1 retrocopy	retro_lafr_289,
Tursiops truncatus	ENSTTRG00000013025	1 retrocopy	retro_ttru_85 ,