RetrogeneDB ID: retro_tgut_16

Retrocopy location

• Organism: Zebrafinch (Taeniopygia guttata)
• Coordinates: 1A:59710010..59711324(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTGUG00000011718
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTGUG00000010655
• Aliases: None
• Description: None

Sequence

>retro_tgut_16
ATGGCGGTGCTGCTGGAGACCACAATGGGCGACCTGGTCATCGACCTGTACACAGAGGAGCGGCCCCGCGCTTGTCTGAA
TTTCCTGAAGCTCTGCAAAGTCAAGTACTACAACTATTGTCTTATTTATAATGTACAGCGGGATTTTATTATACAAACTG
GCGACCCCATGGGAACTGGCCATGGAGGGGAATCCATATTTTTTCAACTGTATGGTGAGCAAGCCAGATTTTTTGAGGCA
GAAAAGGTGCCCAGAATCAAACACAAGAAGAAAGGAACTGTGTCAATGGTGAACAATGGCAGTGATCAGCATGGATCACA
GTTCCTCATTACCACAGGGGAAAACCTGGATTACCTTGATAGTGTACATACAGTATTTGGGGAAGTGACAGAAGGCATGG
ATGTATTGATGAAAATCAATGAAACCTTTGTAGGTAAGGATTTTATCCCATATCAAGATATCAGGATAAATCATACAGTA
ATTTTAGATGATCCCTTTGATGATCCACCTGGCTTGTGTGTTCCTGATCGCTCACCAGAACCTACAAAGGAACAGCTTGA
CAGTGGGAGAATAGGAGCAGATGAAGAAATTGATGACATGAGAGGACGGTCTGCAGATGAAATAGAAGAAGTTCAGGCCG
AAAAAGAAGCAAAAAGTCATGCTATTCTTCTGGAAATGGTGGGAGACTTACCAGATGCAGACATCAAGCCACCAGAAAAT
GTGCTGTTTATCTGTAAGTTGAATCCTGTGACCACAGGTGAAGACCTGGAGATAATATTTTCACGATTTGGTCCCATTAA
AAGTTGCGAAGTGATCCGAGACTGGAAGACTGGTGAATCTCTTTGTTATGCTTTCATTGAGTTTGAAAAGGAGGAAGACT
GTGAGAAAGCCTACTTCAAAATGGACAATGTGCTGATAGATGACAGACGGATACATGTGGATTTTAGCCAGTCTGTTGCA
AAGATTAAATGGAAGGGAAAAGGTGGACAGTATACCAAGGAAGATTCCAAGCACTATGAGAAGGAAGGTGACAAACCTTC
GAAATTTGCTCTGAAAGAAAAAGTAAAACCAAAGCAAGATGGCAAGTATGACCTTGTGCTGGATGAGGATGTAGAGAAGT
CTCACACAAGTCAGTCACACTTGGCTAAAAGAAAGAAGAAGAAAAAGCACCACCACCGTGATGAAGATGACAAGAGGACC
AAAAAATCTAAGGATTCTGACCGAAAGCATGAAGAATGCTGTAGGAAGAGGACCAGGGATATGAAGAAAGACAGGCATCG
AAGCCGTAGCCATTCTCAGGAGAGAGATTACACT

Alignment

ORF - retro_tgut_16 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.27 %
• Parental protein coverage: 91.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAVLLETTVGDLVIDLYTEERPRACLNFLKLCKVKYYNYCLIYNVQRDFIIQTGDPMGTGRGGESIFCQL
          MAVLLETT.GDLVIDLYTEERPRACLNFLKLCKVKYYNYCLIYNVQRDFIIQTGDPMGTG.GGESIF.QL
Retrocopy MAVLLETTMGDLVIDLYTEERPRACLNFLKLCKVKYYNYCLIYNVQRDFIIQTGDPMGTGHGGESIFFQL

Parental  YGDQARFFEAEKVPRIKHKKKGTVSMVNNGSDQHGSQFLITTGENLDYLDGVHTVFGEVTEGMDVLKTIN
          YG.QARFFEAEKVPRIKHKKKGTVSMVNNGSDQHGSQFLITTGENLDYLD.VHTVFGEVTEGMDVL..IN
Retrocopy YGEQARFFEAEKVPRIKHKKKGTVSMVNNGSDQHGSQFLITTGENLDYLDSVHTVFGEVTEGMDVLMKIN

Parental  ETFVDKDFIPYQDIRINHTVILDDPFDDPPGLCVPDRSPEPTKEQLDSGRIGADEEIDDMKGRSAEEIEE
          ETFV.KDFIPYQDIRINHTVILDDPFDDPPGLCVPDRSPEPTKEQLDSGRIGADEEIDDM.GRSA.EIEE
Retrocopy ETFVGKDFIPYQDIRINHTVILDDPFDDPPGLCVPDRSPEPTKEQLDSGRIGADEEIDDMRGRSADEIEE

Parental  VQAEKEAKTRAILLEMVGDLPDADIKPPENVLFVCKLNPVTTGEDLEIIFSRFGPIKSCEVIRDWKTGES
          VQAEKEAK..AILLEMVGDLPDADIKPPENVLF.CKLNPVTTGEDLEIIFSRFGPIKSCEVIRDWKTGES
Retrocopy VQAEKEAKSHAILLEMVGDLPDADIKPPENVLFICKLNPVTTGEDLEIIFSRFGPIKSCEVIRDWKTGES

Parental  LCYAFIEFEKEEDCEKAYFKMDNVLIDDRRIHVDFSQSVAKIKWKGKGGRYTKEDFKDYEKERDKPSKFA
          LCYAFIEFEKEEDCEKAYFKMDNVLIDDRRIHVDFSQSVAKIKWKGKGG.YTKED.K.YEKE.DKPSKFA
Retrocopy LCYAFIEFEKEEDCEKAYFKMDNVLIDDRRIHVDFSQSVAKIKWKGKGGQYTKEDSKHYEKEGDKPSKFA

Parental  LKEKAKPKQDAKYDLVLDEDVEESHTSQSHLAKKQKKKKHHHSEDEDDDKRTKKSKDSDRKHEERCRERS
          LKEK.KPKQD.KYDLVLDEDVE.SHTSQSHLAK..KKKKHHH.....DDKRTKKSKDSDRKHEE.CR.R.
Retrocopy LKEKVKPKQDGKYDLVLDEDVEKSHTSQSHLAKRKKKKKHHHR--DEDDKRTKKSKDSDRKHEECCRKRT

Parental  KSEKKDRHRSRSRSQERDYT
          ...KKDRHRSRS.SQERDYT
Retrocopy RDMKKDRHRSRSHSQERDYT

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_16 retrocopy.

TSS

Taeniopygia guttata was not studied using FANTOM5 data.

Lab

retro_tgut_16 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_tgut_16 has 0 orthologous retrocopies within neognath group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019613	1 retrocopy	retro_cjac_2963,
Macaca mulatta	ENSMMUG00000023067	1 retrocopy	retro_mmul_1715,
Nomascus leucogenys	ENSNLEG00000015316	1 retrocopy	retro_nleu_173,
Oryctolagus cuniculus	ENSOCUG00000007696	2 retrocopies	retro_ocun_661, retro_ocun_892,
Taeniopygia guttata	ENSTGUG00000010655	1 retrocopy	retro_tgut_16 ,