RetrogeneDB ID: retro_ttru_1135

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_105274:19751..20129(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PCBD2
• Ensembl ID: ENSTTRG00000016874
• Aliases: None
• Description: pterin-4 alpha-carbinolamine dehydratase/dimerization cofactor of hepatocyte nuclear factor 1 alpha (TCF1) 2 [Source:HGNC Symbol;Acc:24474]

Sequence

>retro_ttru_1135
GCGCTGGGGGCGCAGGAGGCGACGTGGCGCTGGCCCGTGGGGCTTCGGGGCAGGAGCCAGAGCCTCACGGCCACGTCAGC
AGATGCTCACTCGTTGACAGCAGAGGAGAGGAACCAAGTTATACTTGACCTTAAAGCAGCACGATGGTCGGAATTAAGTG
AGAGAGATGCCATCTACAAAGAGTTCTCTTTCAAACATTTTAATCAGGCATTTGGCTTTATGTCCTGAGTTGCCCTGCAA
GCAGAGAAGATGAATCATCACCCGGAGTAGCTCAACGTGTACAACAAGGTCCAGATAACTCTCTCATCGCATGACGGCAG
AGGACTGACCAAAAGAGATGTGAAACTGGCCAAGTTTAGCGAAAAAGCAGCTGCTTCT

Alignment

ORF - retro_ttru_1135 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.71 %
• Parental protein coverage: 97.67 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ALGARGATRRWFAALRGRSQSLAAMSADAHWLTAEERNQVILDLKAAGWSELSERDAIYKEFSFKNFNQA
          ALGA..AT.RW...LRGRSQSL.A.SADAH.LTAEERNQVILDLKAA.WSELSERDAIYKEFSFK.FNQA
Retrocopy ALGAQEATWRWPVGLRGRSQSLTATSADAHSLTAEERNQVILDLKAARWSELSERDAIYKEFSFKHFNQA

Parental  FGFMSRVALQAEKMNHHPEWFNVYNKVQITLTSHDCGGLTKRDVKLAKFIEKAAAS
          FGFMS.VALQAEKMNHHPE..NVYNKVQITL.SHD..GLTKRDVKLAKF.EKAAAS
Retrocopy FGFMS*VALQAEKMNHHPE*LNVYNKVQITLSSHDGRGLTKRDVKLAKFSEKAAAS

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_1135 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1135 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 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000019125	2 retrocopies	retro_dnov_645, retro_dnov_660,
Equus caballus	ENSECAG00000015810	2 retrocopies	retro_ecab_489, retro_ecab_871,
Erinaceus europaeus	ENSEEUG00000007051	1 retrocopy	retro_eeur_190,
Echinops telfairi	ENSETEG00000016658	2 retrocopies	retro_etel_1252, retro_etel_75,
Macropus eugenii	ENSMEUG00000003784	1 retrocopy	retro_meug_1185,
Myotis lucifugus	ENSMLUG00000012638	1 retrocopy	retro_mluc_1445,
Monodelphis domestica	ENSMODG00000014351	1 retrocopy	retro_mdom_1369,
Pteropus vampyrus	ENSPVAG00000000384	2 retrocopies	retro_pvam_63, retro_pvam_750,
Tursiops truncatus	ENSTTRG00000005775	1 retrocopy	retro_ttru_1541,
Tursiops truncatus	ENSTTRG00000016874	3 retrocopies	retro_ttru_1135 , retro_ttru_359, retro_ttru_511,