RetrogeneDB ID: retro_ttru_1747

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_89741:9978..10569(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHAC1
• Ensembl ID: ENSTTRG00000011476
• Aliases: None
• Description: ChaC, cation transport regulator homolog 1 (E. coli) [Source:HGNC Symbol;Acc:28680]

Sequence

>retro_ttru_1747
CCAGAACACCCCACCCCCCAGGACGACGGCGGCCCCCAAGCGCTGTGGATTTCCGGGTACGGCTCCCTGGTGTGGAGGCC
TGACTTTGCCTACAGCAACAGTCGTGTGGTCTTCGTGCACCACTACAGCAGCCGCCTCTGACAGGGAGACACCTTCCATC
AGGGCAGCGACAAGATGCCTGGTCGTGTGGTGACCCTCCCTGAAGATCGTGAGGGCTGCACTTGGGGTGTGGCGTACCAG
GTGCAAGGTGAGCAGGTCAATGAGGCCCTGAAGTACTTGAACGTGTGGGAGGCAGTGCTTGGTAGCTATGATACCAAGGA
GGTCACCTTCTGCCCTCAAGATGCCCCTGACCAACCACTCAAGGCACTGGCCTACGTGGCCACCCCGCAGAACCCTGGTT
ACCTGGGCCCTGCGCCTGAGGAGGCCATTGCTACGCAGATCCTGGCCTGCTGAGGCTTCTCTGGCCACAGTCTTGAGTAC
TTGCTGCGCCTGGCAGACTTCAGGCAGCTCTGTGGGCCCCAGGCACAGGACGAGCACCTGGCAGCCATCGTGGATGCTGT
AGGCACCATGCTGCCCTGCTTCTGCCCCACT

Alignment

ORF - retro_ttru_1747 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.29 %
• Parental protein coverage: 92.86 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PPSQHPQDDCDPQALWIFGYGSLVWRPDFAYSDSRVGFVRGYSRRFWQGDTFHRGSDKMPGRVVTLLEDR
          P....PQDD..PQALWI.GYGSLVWRPDFAYS.SRV.FV..YS.R..QGDTFH.GSDKMPGRVVTL.EDR
Retrocopy PEHPTPQDDGGPQALWISGYGSLVWRPDFAYSNSRVVFVHHYSSRL*QGDTFHQGSDKMPGRVVTLPEDR

Parental  EGCTWGVAYQVQGEQVNEALKYLNVREAVLGSYDTKEVTFYPQDTPDQPLKALAYVATPQNPGYLGPAPE
          EGCTWGVAYQVQGEQVNEALKYLNV.EAVLGSYDTKEVTF.PQD.PDQPLKALAYVATPQNPGYLGPAPE
Retrocopy EGCTWGVAYQVQGEQVNEALKYLNVWEAVLGSYDTKEVTFCPQDAPDQPLKALAYVATPQNPGYLGPAPE

Parental  EAIATQILVCRGFSGHNLEYLLRLTDFMQLCGPQAQDEHLAAI-DA-STMLPCFCPT
          EAIATQIL.C.GFSGH.LEYLLRL.DF.QLCGPQAQDEHLAAI.DA..TMLPCFCPT
Retrocopy EAIATQILAC*GFSGHSLEYLLRLADFRQLCGPQAQDEHLAAIVDAVGTMLPCFCPT

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_1747 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1747 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000017531	1 retrocopy	retro_dnov_438,
Otolemur garnettii	ENSOGAG00000024541	1 retrocopy	retro_ogar_3206,
Tursiops truncatus	ENSTTRG00000011476	2 retrocopies	retro_ttru_1747 , retro_ttru_945,