RetrogeneDB ID: retro_ttru_1838

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_93857:66515..67555(-)
• Located in intron of: None

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_1838
ATTGCCCTTAGCCCCAATAACCATGAAGTCCACATCTATAAGAAGTTGGGAGCCAGTGGGTGAAAATTCATGAACTCAAG
CAGCACAATGGACACATCACAGGTATCGACTGCACTCCCAAGAGTGACCTCATGGTCACTTGAGGGGCTGACCGCAACGC
CTAGGTCTGGAGTCAGAAAGATGGTATCTGGAAGCCAACCGTGGTGATCCTGAGAATTAACAATGCAGCCACTTCTGTCA
AGTGGTCCCCACTACAGAACAAATTTGTTGTGGGCAGTGGAGCATGACTCATTTCTGTTTGTTACTTCGAGTCCAAAAAT
GACTGGCGAATAAGCAAGCACATTAAAAAACCCATTCGCTCCACAGTTCTCAGCTTGGACTGGCATCCCAACAATGTCTT
GCTGGCAGGAGGATCCTGTGATTTCAAATGCAGAGTGTTTTCTGCCTACATTAAAGAAGTGGATGAGAAGCCAGCCAGTA
CACCCTGGGGCAGCAAGATGCCTTTTGGTCAGCTGATGTCAGCGTTTGGTGGCAGTGGCACTGGCAGCTGGGTGCATGGG
GTCAACTTCTCCGCCAGCAGGAGCCACCTGGCCTGGGTCAGCCACAACACGGTGTCCGTTGCCGATGCCTCAAAAAGTGT
GCAGGTCTCAACTCTGAAGACAGAGTTCCTGCCCCTCCTGAGTGTGTCCTTCATCTCGGAGAACAGCATCATGGCTGCTG
GCCATGACTGCTGCCCCATGCTCTTTAGATGCAACGACTGCAGCTGCTTGACCTTCGTCTCCAAGCTAGACATCCCAAAA
CAGCGCATCCAGCACAACATGTCGGCCATGGAGCACTTCCGCAACATGGACAAGCGGGCCACAACTGAGAACCACAACAA
GGCCCTGGGGATGCTGCACCAGAGCAGCATCACTCAAGTGTCTATTTATGAAGTGGACAAGTAAGATTGTCGCAAATTTT
GCACTACTGGCATCGACAGAGCCATGACCATTTGGCATTTCAAGACCTTAGAGTCTTCTGTCCAGGGCCTTCAGATAATG

Alignment

ORF - retro_ttru_1838 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.67 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IALSPNNHEVHIYKKNG-SQWVKAHELKEHNGHITGIDWAPKSDRIVTCGADRNAYVWSQKDGVWKPTLV
          IALSPNNHEVHIYKK.G.SQWVK.HELK.HNGHITGID..PKSD..VT.GADRNA.VWSQKDG.WKPT.V
Retrocopy IALSPNNHEVHIYKKLG<SQWVKIHELKQHNGHITGIDCTPKSDLMVT*GADRNA*VWSQKDGIWKPTVV

Parental  ILRINRAATFVKWSPLENKFAVGSGARLISVCYFESENDWWVSKHIKKPIRSTVLSLDWHPNNVLLAAGS
          ILRIN.AAT.VKWSPL.NKF.VGSGA.LISVCYFES.NDW..SKHIKKPIRSTVLSLDWHPNNVLLA.GS
Retrocopy ILRINNAATSVKWSPLQNKFVVGSGA*LISVCYFESKNDWRISKHIKKPIRSTVLSLDWHPNNVLLAGGS

Parental  CDFKCRVFSAYIKEVDEKPASTPWGSKMPFGQLMSEFGGSGTGGWVHGVSFSASGSRLAWVSHDSTVSVA
          CDFKCRVFSAYIKEVDEKPASTPWGSKMPFGQLMS.FGGSGTG.WVHGV.FSAS.S.LAWVSH..TVSVA
Retrocopy CDFKCRVFSAYIKEVDEKPASTPWGSKMPFGQLMSAFGGSGTGSWVHGVNFSASRSHLAWVSH-NTVSVA

Parental  DASKSVQVSTLKTEFLPLLSVRFVSENSVVAAGHDCCPMLFSCDDRGCLTFVSKLDIPKQSIQRNMSAME
          DASKSVQVSTLKTEFLPLLSV.F.SENS..AAGHDCCPMLF.C.D..CLTFVSKLDIPKQ.IQ.NMSAME
Retrocopy DASKSVQVSTLKTEFLPLLSVSFISENSIMAAGHDCCPMLFRCNDCSCLTFVSKLDIPKQRIQHNMSAME

Parental  RFRNMDKRATTEDRNTALETLHQNSITQVSIYEVDKQDCRKFCTTGIDGAMTIWDFKTLESSIQGLRIM
          .FRNMDKRATTE..N.AL..LHQ.SITQVSIYEVDK.DCRKFCTTGID.AMTIW.FKTLESS.QGL.IM
Retrocopy HFRNMDKRATTENHNKALGMLHQSSITQVSIYEVDK*DCRKFCTTGIDRAMTIWHFKTLESSVQGLQIM

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_1838 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1838 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,