RetrogeneDB ID: retro_ttru_398

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_214:288551..289906(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNX4
• Ensembl ID: ENSTTRG00000014983
• Aliases: None
• Description: sorting nexin 4 [Source:HGNC Symbol;Acc:11175]

Sequence

>retro_ttru_398
ATGCAGCACGCACCTCCCGATCCCAAGCGGCTTTTGCAGCCTGAGCCCCTAGAGCTGGGCCACCCCGACCCTGGGCTGGA
GTCTGTGGCCAGTGAGGAAGCGGAGGGGGCCCAGGACGAGGGCCCCCGGGGACGGCACAATGACAGAAAATAATTTTCGG
TTGAAGAAGATAGAAATTAATGTTTCAGAAGCAGAAAAGCAAACTGGAAGAAATGCCATGAACATTCAAGAAATATATAC
TGCTTACCTCATTGAAACAAGGTCAGTTGAACATATTGATGGTCAGAGTGTCCTAGCAGACTCACTCTGGAGGCAGTAGA
GTGAATCTGAGTTGTTGAGAAACTACCTTTTAGTATACTATCCACATATTGTTGTGCCACCTCTACCAGAAGAGCGAGCA
GAATGTGTTTGGCATAAACTCTCTGCTGACAACACTGACAAGGATTTCATGGAAAGACAATGAATTGGTTTAGAAAATTT
CCTCTTGAGAGTTGCTTCATATCCCGTCCTCTGTAGAGACATAATCTTCTATTTGTTTTTAACACAGGCAGGCAACTGGA
AGGAGACTGTGAATGAAACAGGATTTCAGCTGAAGGCAGACTGCAGGTTAAAAGCGTTTAATGCAACATTCAGAGTGAAA
AACCCAGACAAGAGATGTACTGAACTAAAACACTACAGTGATGAACTACAGTCTGTCATCGCATATCTTCTTCGAGTCAG
AGCGAGAGTAGCAGATCGACTGTATGGTGTATATACAGTATATGGGAATTACGGGCGAGTTTTTGGTGAGTGGAGTGCCG
TAGAAAAAAGAAATGGGTGATGGACTGCAGAGTGCTGCTCATCATAGGGAGGTGTATGCATCTTCTATCGATTATATTTT
GGAAGATGAAGAACATTATGCAGATCAGTTAAAGGAGTACCTTTTTTATGCAGAAGCCATGCATACAATGCGGGCTGTGT
GCAGGAAACATGAACTTATGCAGTATGACTTGGAGATGGCTGCTCAGGACTTAGCATCCAAGAAGCAGCAGTGTGACAAA
CTGGCAACTGGGACCCTGAGAACATTTTCTTTGAAGGGAATGACTACCAAGCTCTTTGGTCAAGAAACTCCAGAGCAGAG
AGATGCCAGAATAAAGGTGCTAGAAGAACAAATAAATGAAGGAGAACAACTTAACTCTAAAAATCTGGAAGGCAGAGAAT
TTGTCAGAAATGCTTGGGCTGATATTGAACACTTCAAAGAACAAAAGAACCGTGATTTAAAGGAGGCCCTCATAAGCTAT
GCAGTCATGCAGATCAGTATATGCAAAAAGGGAATTGAAGTTTGGACCAATGCTGAGGAATGCTTTAGCAAGATA

Alignment

ORF - retro_ttru_398 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.05 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MEQALPDPERRLQPAPLEPLGHPDAGLESAVGEEAEGARDEGP-GDGSMMENNFWLKKIEISVSEAEKRT
          M..A.PDP.R.LQP.PLE.LGHPD.GLES...EEAEGA.DEGP.GDG.M.ENNF.LKKIEI.VSEAEK.T
Retrocopy MQHAPPDPKRLLQPEPLE-LGHPDPGLESVASEEAEGAQDEGP>GDGTMTENNFRLKKIEINVSEAEKQT

Parental  GRNAMNMQETYTAYLIETRSVEHIDGQSVLTDSLWRRYSEFELLRNYLLVYYPHIVVPPLPEKRAEFVWH
          GRNAMN.QE.YTAYLIETRSVEHIDGQSVL.DSLWR..SE.ELLRNYLLVYYPHIVVPPLPE.RAE.VWH
Retrocopy GRNAMNIQEIYTAYLIETRSVEHIDGQSVLADSLWRQ*SESELLRNYLLVYYPHIVVPPLPEERAECVWH

Parental  KLSADNMDPDFVERRRIGLENFLLRVASHPILCRDKIFYL-LTQEGNWKETVNETGFQLKADSRLKALNA
          KLSADN.D.DF.ER..IGLENFLLRVAS.P.LCRD.IFYL.LTQ.GNWKETVNETGFQLKAD.RLKA.NA
Retrocopy KLSADNTDKDFMERQ*IGLENFLLRVASYPVLCRDIIFYLFLTQAGNWKETVNETGFQLKADCRLKAFNA

Parental  TFRVKNPDKRFTELKHYSDELQSVISHLLRVRARVADRLYGVYKVHGNYGRVFSEWSAIE-KEMGDGLQS
          TFRVKNPDKR.TELKHYSDELQSVI..LLRVRARVADRLYGVY.V.GNYGRVF.EWSA.E.KEMGDGLQS
Retrocopy TFRVKNPDKRCTELKHYSDELQSVIAYLLRVRARVADRLYGVYTVYGNYGRVFGEWSAVE>KEMGDGLQS

Parental  AGHHMDVYASSIDDILEDEEHYADQLKEYLFYAEA---LRAVCRKHELMQYDLEMAAQDLASKKQQCEEL
          A.HH..VYASSID.ILEDEEHYADQLKEYLFYAEA....RAVCRKHELMQYDLEMAAQDLASKKQQC..L
Retrocopy AAHHREVYASSIDYILEDEEHYADQLKEYLFYAEAMHTMRAVCRKHELMQYDLEMAAQDLASKKQQCDKL

Parental  ATGTVRTFSLKGMTTKLFGQETPEQREARIKVLEEQINEGEQQLKSKNQEGREFVKNAWADIERFKEQKN
          ATGT.RTFSLKGMTTKLFGQETPEQR.ARIKVLEEQINEGE.QL.SKN.EGREFV.NAWADIE.FKEQKN
Retrocopy ATGTLRTFSLKGMTTKLFGQETPEQRDARIKVLEEQINEGE-QLNSKNLEGREFVRNAWADIEHFKEQKN

Parental  HDLKEALISYAVMQISMCKKGIQVWTNAKECFSKM
          .DLKEALISYAVMQIS.CKKGI.VWTNA.ECFSK.
Retrocopy RDLKEALISYAVMQISICKKGIEVWTNAEECFSKI

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_398 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_398 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000022808	1 retrocopy	retro_mmus_1627,
Sarcophilus harrisii	ENSSHAG00000000917	1 retrocopy	retro_shar_818,
Tursiops truncatus	ENSTTRG00000014983	1 retrocopy	retro_ttru_398 ,