RetrogeneDB ID: retro_ttru_575

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_2722:42106..43150(-)
• Located in intron of: ENSTTRG00000009644

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARPC1A
• Ensembl ID: ENSTTRG00000003002
• Aliases: None
• Description: actin related protein 2/3 complex, subunit 1A, 41kDa [Source:HGNC Symbol;Acc:703]

Sequence

>retro_ttru_575
ATTGCCCTTAGCCCCAAAAACCACTAAGTCCACATCTATGAGAAGAACGGGAGCCAGTGGGTGAAAGCTCATGAACTCAA
GGAGCACAGCAGACACATCACAGGTATCGACTGGGCTCCCAAGAGTGACCGCGTCGTCACTTGTGGGCCTGACCGCAATG
CCTACGTGTGGAATCAGAAAGATGGTGTCTGGAAGCCGACCCTTGGTGATCCTGAGAATTAACCGTGCAGCCACTTTTGT
CAAGTGGTCCCCGCTACAGAACAAATTTGCTGTGGGTAGCGGAGCACGACTCATTTCTGTTTGTTACTTTGAGTCCGAAA
ATGACCGGTGGGTAAGCAAGCACAGTAAAAAACCCATTCGCTCCATGGTCCTCAGCTTGGATTGGCATCCCAACAACGTC
TTGCTGGCAGCAGGATCGTGTGATTTCAAAGGCAGAGTGTTTTTTGCCTACATTAAAGAAGTGGATGAGAAGCCAGCCAG
TACGTCCTGGGGCAGCAAGATGCCTTTTGGTCAGCTGATGTCAGAGTTTGGTGGCAGTGGCACTGGCGGCTGGGTGCACG
GGGTCAGCTTCTCCGCCAGCGGGAGCCGCCTGGCCTGGGTCAGCCACGACAGCACCGTGTCCGTTGCTGATGCCTCAAAA
GTGTGCAGGTCTCAACTCTGAAGACAGAGTTCCTGCCCCTCCTGAGTGTGCGCTTCGTCTCGGAAAACAGCGTCGTGGCC
GCCGGCCGTGACTGCTGCCCCATGCTCTTTAGCTGCGCCGACCGCGGCTGCTTGACCTTCGTCTCCAAGCTAGACATCCC
GAAACAGAGCATCCAACGCAACATGTCGGCCATGGAGCGCTTCCGCAACATTGGCAGGCGGGCCAAAACCGAGGACCGCA
ACACGGCCCTGGAGACGCTGCACCAGAACAGCATCACTCAAGTGTCTATTTATGAGGTGGACAAGCAAGATTGTCGCAAA
TTTTGCACTACTGGCATCGATGGAGCCATGACCATTTGGGATGTCAAGACCTTAGAGTCTTCTATCCAGGGCCTTCGGAT
AATG

Alignment

ORF - retro_ttru_575 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.14 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IALSPNNHEVHIYKKNGSQWVKAHELKEHNGHITGIDWAPKSDRIVTCGADRNAYVWSQKDGVWKPTL-V
          IALSP.NH.VHIY.KNGSQWVKAHELKEH..HITGIDWAPKSDR.VTCG.DRNAYVW.QKDGVWKPTL.V
Retrocopy IALSPKNH*VHIYEKNGSQWVKAHELKEHSRHITGIDWAPKSDRVVTCGPDRNAYVWNQKDGVWKPTL>V

Parental  ILRINRAATFVKWSPLENKFAVGSGARLISVCYFESENDWWVSKHIKKPIRSTVLSLDWHPNNVLLAAGS
          ILRINRAATFVKWSPL.NKFAVGSGARLISVCYFESEND.WVSKH.KKPIRS.VLSLDWHPNNVLLAAGS
Retrocopy ILRINRAATFVKWSPLQNKFAVGSGARLISVCYFESENDRWVSKHSKKPIRSMVLSLDWHPNNVLLAAGS

Parental  CDFKCRVFSAYIKEVDEKPASTPWGSKMPFGQLMSEFGGSGTGGWVHGVSFSASGSRLAWVSHDSTVSVA
          CDFK.RVF.AYIKEVDEKPAST.WGSKMPFGQLMSEFGGSGTGGWVHGVSFSASGSRLAWVSHDSTVSVA
Retrocopy CDFKGRVFFAYIKEVDEKPASTSWGSKMPFGQLMSEFGGSGTGGWVHGVSFSASGSRLAWVSHDSTVSVA

Parental  DASK-SVQVSTLKTEFLPLLSVRFVSENSVVAAGHDCCPMLFSCDDRGCLTFVSKLDIPKQSIQRNMSAM
          DASK.SVQVSTLKTEFLPLLSVRFVSENSVVAAG.DCCPMLFSC.DRGCLTFVSKLDIPKQSIQRNMSAM
Retrocopy DASK<SVQVSTLKTEFLPLLSVRFVSENSVVAAGRDCCPMLFSCADRGCLTFVSKLDIPKQSIQRNMSAM

Parental  ERFRNMDKRATTEDRNTALETLHQNSITQVSIYEVDKQDCRKFCTTGIDGAMTIWDFKTLESSIQGLRIM
          ERFRN...RA.TEDRNTALETLHQNSITQVSIYEVDKQDCRKFCTTGIDGAMTIWD.KTLESSIQGLRIM
Retrocopy ERFRNIGRRAKTEDRNTALETLHQNSITQVSIYEVDKQDCRKFCTTGIDGAMTIWDVKTLESSIQGLRIM

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_575 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_575 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 7 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000005984	5 retrocopies	retro_dnov_1615, retro_dnov_1839, retro_dnov_1966, retro_dnov_2257, retro_dnov_941,
Macropus eugenii	ENSMEUG00000005609	8 retrocopies	retro_meug_1033, retro_meug_1081, retro_meug_1495, retro_meug_1668, retro_meug_1755, retro_meug_1912, retro_meug_2179, retro_meug_492,
Monodelphis domestica	ENSMODG00000001303	9 retrocopies	retro_mdom_1360, retro_mdom_1380, retro_mdom_1438, retro_mdom_1551, retro_mdom_1796, retro_mdom_1917, retro_mdom_686, retro_mdom_699, retro_mdom_808,
Oryctolagus cuniculus	ENSOCUG00000003944	1 retrocopy	retro_ocun_1130,
Sarcophilus harrisii	ENSSHAG00000010673	2 retrocopies	retro_shar_180, retro_shar_727,
Sus scrofa	ENSSSCG00000007609	1 retrocopy	retro_sscr_387,
Tursiops truncatus	ENSTTRG00000003002	4 retrocopies	retro_ttru_1621, retro_ttru_1838, retro_ttru_575 , retro_ttru_853,