RetrogeneDB ID: retro_ttru_1687

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_85739:28952..30202(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTTRG00000003794
• Aliases: None
• Description: None

Sequence

>retro_ttru_1687
GAACCCTTTGTCCCTGACGTGGTGAATGAGGTGCAGGTGAAGGCAGACAGACCGAACCCCTGGATGTTCAGGAATCACTC
AGGTGACACAAAAGAGGCTGAGGTCCAGGGGGACCCTGAAGAACTTGCAGAGCCTGCAGCCCGGAGGCTCCTGAAAGTGA
GGAAGAAGGACCAGTGGTGGCGGAAGAAATTCTGTTGAAAGAATTTGAGGAAAGGCGATCACTTTGACAAAAGTCTGGGC
TCAACCAGATCGCCAAGCCGGTGGGCAGTCAAGAAGCAAAAGATCTTAGCAGCCAGGAGGTGCTGTCTGAATTGAGGGCA
CTGACTCAGAAACTCAACAGGGAGAGCCATCAGTCCAGGAAGCAAGAACTGAGTTCAACGAGGACAGTTCTGGCGGTCCA
GAGAGAGGAACCTGCCGGGGAGGAAGAGGAGCCTCTGTTGCTGCAGAGGCCGGAGAGAGCACGAGCTCTGGAGGAACTGG
AGGAACTGGGCAAAGAAGGATGTTTTCAAAACAAGGAGCTTCCCAGAGCTGCGGTAGAAGGGCAGCAGTTGGAGAGGAAC
CCAAGTAATCATCTTGGTGTCCCCAAGGAGAAGAAAAGGAAGGAGCAAATGATTGATCTCCAGAACCTCCTGACCACAAA
ATCTCCTTCCATGAAGTCCTTGGCAGTTCCCACGACAGTAGAGGAGTTGGAAGATGAAGAGAGAGATCAAAGGCAGATGA
TAAAGGAAGCTTTTGCTGGGAATGATGTCATCAGAGACTTCTTGAAAGAGAAGAGGGAAGCTGTGGAGGCGAGTAAGCCG
AAGGATGTGGACCTGACTCCGCCTGGCTGGGGCGAGTGGGGTGGTGTGGGCCTGAAGCCCAGTGCAAAGAAGAGACGCCG
GTTTCTCATTAAAGCCCCTGAGGGTCCTCCAAGGAAAGACAAGAATTTGCCAAATGTGATTCTCAATGAGAAGCGCAACA
TCCATGCAGTGGCTCATCAGGTGCGGATGCTTCCATATCCATTCACACACCATCAGCAATTTGAAAGGACCATTCAGACC
CCTATAGGATCTACATGGAACCCCCAGAGGTCCTTCCAAAAGCTGACTATGCCCAAGGTTGCCACCAAGCCGGGCCATAT
CATTAAGCCTATAAAAGCAGAGGATGTGGGCTGCCGGTCTTCCTCAAGGTCGGACCTCTCTGTCGTACAGAGAAATCCAA
AATGACTCTCCATACGTCACAAAAAACAGCTGAAGAAAAACTCTGTAGAT

Alignment

ORF - retro_ttru_1687 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.74 %
• Parental protein coverage: 54.8 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EPFVPDVVNEVQVKADRPNPWMFRNHSGDTKEAEVQGDPEELAEPAAQ-EAPESEEEGPVVAEEILLKEF
          EPFVPDVVNEVQVKADRPNPWMFRNHSGDTKEAEVQGDPEELAEPAA..EAPESEEEGPVVAEEILLKEF
Retrocopy EPFVPDVVNEVQVKADRPNPWMFRNHSGDTKEAEVQGDPEELAEPAAR<EAPESEEEGPVVAEEILLKEF

Parental  EERRSLRQKSGLNQIAKPVGSQEAKDLSSQEVLSELRALSQKLNRESHQSRKQELSSTRTVLAVQREEPA
          EERRSL.QKSGLNQIAKPVGSQEAKDLSSQEVLSELRAL.QKLNRESHQSRKQELSSTRTVLAVQREEPA
Retrocopy EERRSL*QKSGLNQIAKPVGSQEAKDLSSQEVLSELRALTQKLNRESHQSRKQELSSTRTVLAVQREEPA

Parental  GEEEEPLLLQRPERARTLDELEELGKEGCFQNKELPRVVVEGQQLERNPSNHLGVPKEKKRKEQMIDLQN
          GEEEEPLLLQRPERAR.........KEGCFQNKELPR..VEGQQLERNPSNHLGVPKEKKRKEQMIDLQN
Retrocopy GEEEEPLLLQRPERARAXXXXXXXXKEGCFQNKELPRAAVEGQQLERNPSNHLGVPKEKKRKEQMIDLQN

Parental  LLTTKSPSMKSLAVPTTVEELEDEERDQRQMIKEAFAGDDVIRDFLKEKREAVEASKPKDVDLTLPGWGE
          LLTTKSPSMKSLAVPTTVEELEDEERDQRQMIKEAFAG.DVIRDFLKEKREAVEASKPKDVDLT.PGWGE
Retrocopy LLTTKSPSMKSLAVPTTVEELEDEERDQRQMIKEAFAGNDVIRDFLKEKREAVEASKPKDVDLTPPGWGE

Parental  WGGVGLKPSAKKRRRFLVKAPEGPPRKDKNLPNVILNEKRNIHAVAHQVRMLPYPFTHHQQFERTIQTPI
          WGGVGLKPSAKKRRRFL.KAPEGPPRKDKNLPNVILNEKRNIHAVAHQVRMLPYPFTHHQQFERTIQTPI
Retrocopy WGGVGLKPSAKKRRRFLIKAPEGPPRKDKNLPNVILNEKRNIHAVAHQVRMLPYPFTHHQQFERTIQTPI

Parental  GSTWNTQRSFQKLTMPKVVTKPGHIIKPIKAEDVGYRSSSRSDLSVVQRNPKRLSIRHKKQLKKNSVD
          GSTWN.QRSFQKLTMPKV.TKPGHIIKPIKAEDVG.RSSSRSDLSVVQRNPK.LSIRHKKQLKKNSVD
Retrocopy GSTWNPQRSFQKLTMPKVATKPGHIIKPIKAEDVGCRSSSRSDLSVVQRNPK*LSIRHKKQLKKNSVD

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_1687 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1687 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 14 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013671	2 retrocopies	retro_btau_133, retro_btau_1706,
Cavia porcellus	ENSCPOG00000014231	2 retrocopies	retro_cpor_1272, retro_cpor_242,
Dasypus novemcinctus	ENSDNOG00000002180	1 retrocopy	retro_dnov_1479,
Homo sapiens	ENSG00000156697	1 retrocopy	retro_hsap_29,
Gorilla gorilla	ENSGGOG00000014930	1 retrocopy	retro_ggor_163,
Loxodonta africana	ENSLAFG00000016653	1 retrocopy	retro_lafr_110,
Myotis lucifugus	ENSMLUG00000001984	2 retrocopies	retro_mluc_1643, retro_mluc_308,
Macaca mulatta	ENSMMUG00000020700	1 retrocopy	retro_mmul_35,
Mus musculus	ENSMUSG00000063785	1 retrocopy	retro_mmus_261,
Nomascus leucogenys	ENSNLEG00000015258	1 retrocopy	retro_nleu_2091,
Procavia capensis	ENSPCAG00000006070	1 retrocopy	retro_pcap_127,
Pan troglodytes	ENSPTRG00000022262	1 retrocopy	retro_ptro_824,
Tarsius syrichta	ENSTSYG00000009415	1 retrocopy	retro_tsyr_2104,
Tursiops truncatus	ENSTTRG00000003794	1 retrocopy	retro_ttru_1687 ,