RetrogeneDB ID: retro_ttru_1311

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_110238:210170..210642(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EMC3
• Ensembl ID: ENSTTRG00000007554
• Aliases: None
• Description: ER membrane protein complex subunit 3 [Source:HGNC Symbol;Acc:23999]

Sequence

>retro_ttru_1311
CCCGCTATGCTCATAGACATGATGAAAGGCAACGCCACATGTGTCCTCCCTATGATTCTTATTGGTGGATGGCTCAACAT
GACGTTTTCAGGCTTTGTCACAACCAAGGTCCCGTTTCCACTGACCCTGCCTTTTAAGCCCATGCTACAGCAAGGAATTA
AACTACTCACATTAGATGCCTCCTGGGTGAGTTCTGAATCCTGGTATTTCCTCAATGTCTTTGGGCTTCGGGGCATTTAC
TCTCTGATTTGGGGCCAAGATAATGTTGCTGACCAATCGCGGATGATGCAGGAACAGATGACTGGAGCAGCCATGGCCAT
GCCCGCAGACACCAACAAAGCTTTTAAGACGGTGGGAAGCTTTGGAGCCTACCGACCACCAGTGGGCACTAGATGGCGTC
AAAGAGGAGCTCGTGGCTGAAGACCTCCACTTTGAAGGCATGTTCAAAAAGGAATTACAGACCTCTATTTTT

Alignment

ORF - retro_ttru_1311 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.76 %
• Parental protein coverage: 60. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PTMLTDMMKGNVTNVLPMILIGGWINMTFSGFVTTKVPF-LTL-FKPMLPQGNELLTLDASWVSSASWYF
          P.ML.DMMKGN.T.VLPMILIGGW.NMTFSGFVTTKVPF.LTL.FKPML.QG..LLTLDASWVSS.SWYF
Retrocopy PAMLIDMMKGNATCVLPMILIGGWLNMTFSGFVTTKVPFPLTLPFKPMLQQGIKLLTLDASWVSSESWYF

Parental  LNVFGLRSIYSLILGQDNAADQSRMMQEQMTGAAMAM-PADTNKAFKTEWEALELTDHQWALDDVEEELM
          LNVFGLR.IYSLI.GQDN.ADQSRMMQEQMTGAAMAM.P....K.....WEALE.TDHQWALD.V.EEL.
Retrocopy LNVFGLRGIYSLIWGQDNVADQSRMMQEQMTGAAMAM>PQTPTKLLR-RWEALEPTDHQWALDGVKEELV

Parental  AKDLHFEGMFKKELQTSIF
          A.DLHFEGMFKKELQTSIF
Retrocopy AEDLHFEGMFKKELQTSIF

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_1311 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1311 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 9 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005202	1 retrocopy	retro_cfam_730,
Callithrix jacchus	ENSCJAG00000037305	1 retrocopy	retro_cjac_3209,
Equus caballus	ENSECAG00000024410	1 retrocopy	retro_ecab_737,
Felis catus	ENSFCAG00000024898	2 retrocopies	retro_fcat_1932, retro_fcat_2002,
Microcebus murinus	ENSMICG00000002333	2 retrocopies	retro_mmur_439, retro_mmur_707,
Mustela putorius furo	ENSMPUG00000017149	1 retrocopy	retro_mputfur_456,
Pteropus vampyrus	ENSPVAG00000012615	3 retrocopies	retro_pvam_1260, retro_pvam_1278, retro_pvam_1439,
Tursiops truncatus	ENSTTRG00000007554	2 retrocopies	retro_ttru_1311 , retro_ttru_285,
Vicugna pacos	ENSVPAG00000003247	2 retrocopies	retro_vpac_308, retro_vpac_461,