RetrogeneDB ID: retro_ttru_1421

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_112862:157259..157739(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTTRG00000009478
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DIO1
• Ensembl ID: ENSTTRG00000009105
• Aliases: None
• Description: deiodinase, iodothyronine, type I [Source:HGNC Symbol;Acc:2883]

Sequence

>retro_ttru_1421
GAAGGCGGTCCAGCGCCCAACTCCGAGGTGGTCCTGCCCGACGGCTTCCAGAACCAGCACATCCTCGACTACGCCCGAGG
AAACCGCCCGCTGGTGCTCAATTTCGGTAGCTGCACCTGACCACCGTTCATGGCGCGGATGAGCGCCTTCCAGCGCCTGG
TCACCAAGTATCAGCGCGACGTCGACTTCCTCATCATCTACATTGAGGAAGCGCACCCCTCGGACGGCTGGGTCACCACG
GACTCTCCCTACAGCATCCCGCAGCACCGCAGCCTGGAGGACCGGGTCAGCGCAGCGCGGGTACTGCAGCAAGGTGCTCC
CGAATGCTCTCTCGTCCTCGACACCATGGCCAACTCTAGCAGCTCCGCCTACGGCGCCTACTTCGAGCGCCTCTATGTCA
TCCAGAGTGGCACCATTATGTACCAGGGCGGCCGTGGCCCTGATGGCTACCAGGTCTCCGAGCTGCGCACCTGGCTGGAG

Alignment

ORF - retro_ttru_1421 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.62 %
• Parental protein coverage: 63.45 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QGGRAPNCPVVRLSG-QRCNIWDFMQGNRPLVLNFGSCTUPSFIFKFDQFKRLIEDFSSIADFLIIYIEE
          .GG.APN..VV...G.Q...I.D...GNRPLVLNFGSCT.P.F......F.RL........DFLIIYIEE
Retrocopy EGGPAPNSEVVLPDGFQNQHILDYARGNRPLVLNFGSCT*PPFMARMSAFQRLVTKYQRDVDFLIIYIEE

Parental  AHASDGWAFKNN-VDIKNHQHLQDRLRAARLLLDRSPQCPVVVDTMKNQSSQLYAALPERLYVLQDGRIL
          AH.SDGW........I..H..L.DR..AAR.L....P.C..V.DTM.N.SS..Y.A..ERLYV.Q.G.I.
Retrocopy AHPSDGWVTTDSPYSIPQHRSLEDRVSAARVLQQGAPECSLVLDTMANSSSSAYGAYFERLYVIQSGTIM

Parental  YKGKPGPWNYRPEEVRAVLE
          Y.G..GP..Y...E.R..LE
Retrocopy YQGGRGPDGYQVSELRTWLE

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_1421 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1421 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000211452	1 retrocopy	retro_hsap_65,
Gorilla gorilla	ENSGGOG00000015406	1 retrocopy	retro_ggor_1072,
Microcebus murinus	ENSMICG00000014290	1 retrocopy	retro_mmur_1532,
Tursiops truncatus	ENSTTRG00000009105	1 retrocopy	retro_ttru_1421 ,