RetrogeneDB ID: retro_ttru_1621

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_73330:0..670(+)
• 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_1621
ACGGTCCTTCAGCTTGGATTGGATCCCAACAACGTCTTGCTGGCAGCAGGATCCTGTGATTTCAAATGCAGAGTGTTTTC
TGCCTACATTCAAGAAGTGGATGAGAAGCCAGCCAGTACGCCCATGGGGCAGCAAGATGCCTTTTGGTCATCTGATGTCA
GAGTTTGGTGGCAGTGGCCCTGGCGGCTGGGTGCGCAAGGTCAGCTTCTCCGCCAGCGGGAGCCGCCTGGCCTGGGTCAG
CCACGACGGCCCCGTGTCCGTTGCCGATGCCTCAAAAAGCATGCAGATCTCAACTCTGAAGACAGAGTTCCTGCCCCTCC
TGAGTGTGTCCTTCATCTCGGAGGACAGCGTCCTGGCTGCTGGCCATGACTGCTGCCCCATGCTCTTTAGCTGCGCCGAC
CGCGGCTGCTTGACCTTTGTCTCCAAGCTAGACATCCCGAAACAGAGCATCCAGCGCAACGTGTCAGCCACGGAGCGCTT
CTGCAACATGGACAAGCGGGCCACGACCGAGGACCGCAACCCGGCCCTGGAGATGCTGCGCCAGGACAGTATCACTCAAA
TGTCTATTTATGAGGCAGACAGGCAAGATTGTTGCAAATTTTGCACTACTGGCATCGATGGAGCCATGACCTTTTGGGAT
TTCAAGACCTTAGAGTCTTCTATCCAGGGC

Alignment

ORF - retro_ttru_1621 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.16 %
• Parental protein coverage: 64.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TVLSLDWHPNNVLLAAGSCDFKCRVFSAYIKEVDEKPASTP-WGSKMPFGQLMSEFGGSGTGGWVHGVSF
          TVL.L...PNNVLLAAGSCDFKCRVFSAYI.EVDEKPASTP.WGSKMPFG.LMSEFGGSG.GGWV..VSF
Retrocopy TVLQLGLDPNNVLLAAGSCDFKCRVFSAYIQEVDEKPASTP>WGSKMPFGHLMSEFGGSGPGGWVRKVSF

Parental  SASGSRLAWVSHDSTVSVADASKSVQVSTLKTEFLPLLSVRFVSENSVVAAGHDCCPMLFSCDDRGCLTF
          SASGSRLAWVSHD..VSVADASKS.Q.STLKTEFLPLLSV.F.SE.SV.AAGHDCCPMLFSC.DRGCLTF
Retrocopy SASGSRLAWVSHDGPVSVADASKSMQISTLKTEFLPLLSVSFISEDSVLAAGHDCCPMLFSCADRGCLTF

Parental  VSKLDIPKQSIQRNMSAMERFRNMDKRATTEDRNTALETLHQNSITQVSIYEVDKQDCRKFCTTGIDGAM
          VSKLDIPKQSIQRN.SA.ERF.NMDKRATTEDRN.ALE.L.Q.SITQ.SIYE.D.QDC.KFCTTGIDGAM
Retrocopy VSKLDIPKQSIQRNVSATERFCNMDKRATTEDRNPALEMLRQDSITQMSIYEADRQDCCKFCTTGIDGAM

Parental  TIWDFKTLESSIQG
          T.WDFKTLESSIQG
Retrocopy TFWDFKTLESSIQG

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_1621 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1621 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,