RetrogeneDB ID: retro_tgut_24

Retrocopy location

• Organism: Zebrafinch (Taeniopygia guttata)
• Coordinates: 4:50133471..50134649(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTGUG00000006076
• Aliases: None
• Description: None

Sequence

>retro_tgut_24
AGGAAAGCAGCTCTGAAAGCTGCACTGAGAAATAAGATTGAATATGAGAAAAAAGCATTGTCTGTTGTTGAGCAGCTCCT
GGAAGAGGACATTGCTGAAAAGTTCTTTCTAAATTTTGGAAAATGCATTATTCCATTTACTCACTATAAAGATGTTGTTG
ATGAACAGTCTATCATTAAACTGTGTGGTTATCCTCTATGTCAGAATAATCTGAAAAATGTGCCAAAGCAGAAGTACAGA
ATTTCAACAAAAACAAACAGAGTTTATGATATCATTGAAAGAAAGTGCTTTTGCAGCAACTTTTGCTATAGAGCATATAA
ATATTTTGAAACTCAAATTTCCAAAAATCAAGTGTGGATGAGACAAGTAAAACCACAAGACACAGAGATGCTGAAGGAAG
GACGGAGTGGACAGTCTGGAGAAGAGGTGAAACTACATGCTGAAGTAATTAAAGAATTTGACATTGAAAATCCTAGGATA
TCTTCAGATCCATGTGAATCTGGTTCTCATGACACAGACAGTAACAGCAGTACTCAGTACTGATACTGAACAAGGTTTTA
TTTTTTCTGTCCTACCAGGCAGTCAATCAAGTTCAGCCAATTTTGCACAGAAATTGCACAGAAAAAGCATCCTCAAATAG
AAGCATGCTCAGAAAGTCCATGCCAGGCCTAAAACTGAAGATGTAGGTGTGGTAGAATCCAGTGAACAACTATCTAATCA
TGAAGTAGACACTCAGGAAGAAAGACATGTTTGCTCTGTTCAAAATGAAGTAACTGCACCACCTTCAGACAATACTGCTC
CTGAGAAATCAAGTGCTTCAGAAATCTTTGAAAATACATGTGGATCACAAATAGTTTTTCTAGGTGTGAGCAAAAGAGGA
GTAGAACATCTTAAAATAACACTAGCTAACTCAACAGAACATAAAAAACCCTGAACTGAGGCATCCAGTTAATTCCAAAG
GCAGTTTACTAGTGTTGTTTAGGCAACACTTAAGGAATGGAGAGCTGAGGAAACTAAAATTTCTGCATGGCCCAAACTAT
ACTTCTTTGTGCTCATCAGAGTGAATAGGATCTGTCAACCAGGAGACTGAAGAACTTGATGAGAGTGACTTAGATAGAGC
TGATGGTCTCAACACTGTTGCTGTAGGGGAGTCTGAAAACAGTTTGAACCTTTACCTT

Alignment

ORF - retro_tgut_24 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.28 %
• Parental protein coverage: 68.72 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RKAALEAALRKKIECEKKALSIVEQLLEEDITEEFLLNCGKSITP-SHYKDVVDERSIIKLCGYPLCQKR
          RKAAL.AALR.KIE.EKKALS.VEQLLEEDI.E.F.LN.GK.I.P..HYKDVVDE.SIIKLCGYPLCQ..
Retrocopy RKAALKAALRNKIEYEKKALSVVEQLLEEDIAEKFFLNFGKCIIPFTHYKDVVDEQSIIKLCGYPLCQNN

Parental  LENVPKQKYRISTKTNRVYDITERKCFCSNFCYKASKYFEAQISKSPVWMREEEKPPDIELLKEGRSGQS
          L.NVPKQKYRISTKTNRVYDI.ERKCFCSNFCY.A.KYFE.QISK..VWMR...KP.D.E.LKEGRSGQS
Retrocopy LKNVPKQKYRISTKTNRVYDIIERKCFCSNFCYRAYKYFETQISKNQVWMRQV-KPQDTEMLKEGRSGQS

Parental  GEEVKLRDEVIKASDIENPRISSDPCESGSH--DTASDS-STDTEQGFISSVLPGSQSSSASFAQQLHRK
          GEEVKL..EVIK..DIENPRISSDPCESGSH..D..S...STDTEQGFI.SVLPGSQSSSA.FAQ.LHRK
Retrocopy GEEVKLHAEVIKEFDIENPRISSDPCESGSHDTDSNSST>STDTEQGFIFSVLPGSQSSSANFAQKLHRK

Parental  SILKKKHAQKVHTSSKTEDADVVEATEQLSHCKLDTQEERHAFSVHDEVTAPPSDNTAPGKSSASEIFEN
          SILK.KHAQKVH...KTED..VVE..EQLS....DTQEERH..SV..EVTAPPSDNTAP.KSSASEIFEN
Retrocopy SILK*KHAQKVHARPKTEDVGVVESSEQLSNHEVDTQEERHVCSVQNEVTAPPSDNTAPEKSSASEIFEN

Parental  TCGSEIVFLGVSKRGAEHLKRTLAKSTEHK-NPELRHPVNSKGSLLEVLRQTLTEWRTEETLKFLYGPNY
          TCGS.IVFLGVSKRG.EHLK.TLA.STEHK.NPELRHPVNSKGSLL...RQ.L........LKFL.GPNY
Retrocopy TCGSQIVFLGVSKRGVEHLKITLANSTEHK>NPELRHPVNSKGSLLVLFRQHLRNGELRK-LKFLHGPNY

Parental  TSLCSAECIASVNQETEELDEDDLDTADDLNTVGVGESENSLNYSL
          TSLCS.E.I.SVNQETEELDE.DLD.AD.LNTV.VGESENSLN..L
Retrocopy TSLCSSE*IGSVNQETEELDESDLDRADGLNTVAVGESENSLNLYL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Taeniopygia guttata was not studied using RNA-Seq expression data.

ChIP-Seq

Taeniopygia guttata was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tgut_24 retrocopy.

TSS

Taeniopygia guttata was not studied using FANTOM5 data.

Lab

retro_tgut_24 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_tgut_24 has 0 orthologous retrocopies within neognath group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000020158	1 retrocopy	retro_cfam_106,
Myotis lucifugus	ENSMLUG00000001016	1 retrocopy	retro_mluc_262,
Otolemur garnettii	ENSOGAG00000001009	1 retrocopy	retro_ogar_28,
Taeniopygia guttata	ENSTGUG00000006076	1 retrocopy	retro_tgut_24 ,