RetrogeneDB ID: retro_tgut_9

Retrocopy location

• Organism: Zebrafinch (Taeniopygia guttata)
• Coordinates: 1A:59700863..59702033(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTGUG00000011716
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTGUG00000002119
• Aliases: None
• Description: None

Sequence

>retro_tgut_9
ATGGGGAAGTCGGATTTCCTCAGCCCCAAGGCCATCGCCAACTGCATCAAGTCCAAGGGGCTGCAGAAGCTGTGCTGGTA
CTGCCAGATGTGCCAGAAGCAGTGCCGCGATGAGAACAGCTTCAAATGTCACTGCATGTCCGAGTCCCACCAGAAGCAGC
TGCTGCTGGCTTCTGAAAATCCTCAGCAATTCGTGGATTACTTCTCTGAGGAATTCCAAAAGGATTTCCTGGAATTGCTC
AGGAGGCAATTTGGAACAAGGAGAGTCCTCAATAACATTGTGTACAATGAGTACATCAGCCGTCGGGAACACATCCATAT
GAATGCCACGCAATGGGAGACACTCACTGATTTTACAAAGTGGCTGGGGAGAGAAGGTCTTTGCAAGGTAGGTGAGACTC
CTAAAGGCTGGTACATTCAGTACATCGACAGGGACCCAGAGACCATTTGCAGGCAGCAAGAACAAGAGAGGAAGAAGAAA
CAGGACCTTGATGATGAAGAAAAAGCTGCTAAATTCATTGAACAACAAGTTAGAAGAGGTTTGGAGGGGAAAGATGTGGA
AATGCCAGTCTATACGGAATTGAACAGAGAAAACAAAGAAGAAAAAGTTAAATTTAAATTAAACAAAGGAGCAAGTACTT
CAGTTGCAGCATCTTCTAAAACAAGTGTCCTTGGACAAAATGCACTGAAGATGGTAGAGGGTGCAGTGAAAAAAAGACAA
GCAGCTCATTGCTCTGGTCAGCCCAAAGAGAAAAAGAACAAATCTGCACTTGATGAGATCATGGAGCTTGAAGAGGAGAA
AAAAAGAACATCTCGAAGAGACTACTGGTTACAGCCTGAAATCATTGTAAAAATTGTAACAAAAAAGCTAGGAGAGAAAT
ACCACGAGAAGAAGGCAGTTGTTAAGGAAGTGATTGACAGATACACAGCAATTGTGAAGGTGATTGGCTCTGGGGATAAA
CTGAAGCTTGATCAGACACATCTAGAAACTGTAATACCAGCACCAGGCAAGAAAGTACTGGTATTAAATGGTGAGTACAG
GGGAAATGAAGGCATTTTGGAATCCATCAATGAGGAAAGGTTTTCAGTGACAATAACCATCAACTCGGGACCTCTAAAAG
GGCGTAGAGTCGAAGATATCCAGTATGAGGATGTTTCCAAACTTGCCTGA

Alignment

ORF - retro_tgut_9 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.03 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGKSDFLSPKAIANRIKSKGLQKLRWYCQMCQKQCRDENGFKCHCMSESHQRQLLLASENPQQFMDYFSE
          MGKSDFLSPKAIAN.IKSKGLQKL.WYCQMCQKQCRDEN.FKCHCMSESHQ.QLLLASENPQQF.DYFSE
Retrocopy MGKSDFLSPKAIANCIKSKGLQKLCWYCQMCQKQCRDENSFKCHCMSESHQKQLLLASENPQQFVDYFSE

Parental  EFRNDFLELLRRRFGTKRVHNNIVYNEYISHREHIHMNATQWETLTDFTKWLGREGLCKVDETPKGWYIQ
          EF..DFLELLRR.FGT.RV.NNIVYNEYIS.REHIHMNATQWETLTDFTKWLGREGLCKV.ETPKGWYIQ
Retrocopy EFQKDFLELLRRQFGTRRVLNNIVYNEYISRREHIHMNATQWETLTDFTKWLGREGLCKVGETPKGWYIQ

Parental  YIDRDPETIRRQQEQERKKKQDLDDEEKTAKFIEQQVRRGLEGKELEMPVYTELNRENEEEKVTFNLNKG
          YIDRDPETI.RQQEQERKKKQDLDDEEK.AKFIEQQVRRGLEGK..EMPVYTELNREN.EEKV.F.LNKG
Retrocopy YIDRDPETICRQQEQERKKKQDLDDEEKAAKFIEQQVRRGLEGKDVEMPVYTELNRENKEEKVKFKLNKG

Parental  ASTSVAASSKTSSVLGQNALKMVEGAVKRKEAAHSSGQSKEKKKKSALDEIMELEEEKKRTSRRDYWLHP
          ASTSVAASSKT.SVLGQNALKMVEGAVK...AAH.SGQ.KEKK.KSALDEIMELEEEKKRTSRRDYWL.P
Retrocopy ASTSVAASSKT-SVLGQNALKMVEGAVKKRQAAHCSGQPKEKKNKSALDEIMELEEEKKRTSRRDYWLQP

Parental  EIIVKIVTKKLGEKYHKKKAVVKEVIDKYTAVVKVIDSGDKLKLDQTHLETVIPAPGKKVMVLNGGYRGN
          EIIVKIVTKKLGEKYH.KKAVVKEVID.YTA.VKVI.SGDKLKLDQTHLETVIPAPGKKV.VLNG.YRGN
Retrocopy EIIVKIVTKKLGEKYHEKKAVVKEVIDRYTAIVKVIGSGDKLKLDQTHLETVIPAPGKKVLVLNGEYRGN

Parental  EGILESINEKRFSVTITIDSGPLKGRRVEDIQYEDVSKLA
          EGILESINE.RFSVTITI.SGPLKGRRVEDIQYEDVSKLA
Retrocopy EGILESINEERFSVTITINSGPLKGRRVEDIQYEDVSKLA

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_9 retrocopy.

TSS

Taeniopygia guttata was not studied using FANTOM5 data.

Lab

retro_tgut_9 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_tgut_9 has 0 orthologous retrocopies within neognath group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000004280	1 retrocopy	retro_acar_162,
Cavia porcellus	ENSCPOG00000010515	5 retrocopies	retro_cpor_279, retro_cpor_281, retro_cpor_818, retro_cpor_987, retro_cpor_989,
Dipodomys ordii	ENSDORG00000003732	2 retrocopies	retro_dord_344, retro_dord_657,
Ficedula albicollis	ENSFALG00000001842	1 retrocopy	retro_falb_26,
Myotis lucifugus	ENSMLUG00000002261	1 retrocopy	retro_mluc_1186,
Rattus norvegicus	ENSRNOG00000026690	1 retrocopy	retro_rnor_2665,
Taeniopygia guttata	ENSTGUG00000002119	1 retrocopy	retro_tgut_9 ,