RetrogeneDB ID: retro_drer_1

Retrocopy location

• Organism: Zebrafish (Danio rerio)
• Coordinates: 10:7156933..7157675(-)
• Located in intron of: ENSDARG00000053443

Retrocopy information

• Ensembl ID: ENSDARG00000094312
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: ndufa9
• Ensembl ID: ENSDARG00000070723
• Aliases: ndufa9, wu:fc41f12, zgc:112513
• Description: NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 9 [Source:ZFIN;Acc:ZDB-GENE-050320-20]

Sequence

>retro_drer_1
GTTTGACAGACTCAGCATTACTATGGCTCTGACGGCCATAATCATGGCGTCTGTCACACTGATTTGCCGTCCTGCGGGTA
TCCTTCCCAAGCTTTCAGGCACCTGTTCTCCGGTGTTGCTGGCAGCAGCTCCTGTGACGGTACAGCAGAGGAAGATTCAT
CATGCCGTAGTGCCCAGTGGAAAAGGAGGCCGCTCTTCCTTTAGTGGACTCGCTGCCACTGTTTTTGGAGCCACTGGCTT
TCTTGGCCGATATGTTGTCAACCGTCTAGGACGTATGGGTTCCCAGGTTGTGATCCCTTACCGATGTGACCAGTATGATC
TCATGTACCTCAGACCTATGGGCGATTTGGGACAGATCATCTTTATGGAATGGGATCCAAGAAACAAGGAGTCAATTCAA
AGAGCAATCTCTCACTCCAACGTGGTGATCAACCTTGTCGGAAGAGAATGGGAGACCAGCAACTACAAGTATGAAGATGT
GTTCGTCTCCATCCCTCTGCAGATTGCGAAGGCAACTCGTGAAGCTGGAATTAAAAAGTTCATTCATATGTCGCACCTTA
ACGCAGACATTCGCAGCCCCTCCAAGTATCTGAGAAATAAGGCAGTCGGTGAGGAGGCTGTGAGAAACGAGTTCCCTGAT
GCCATCATTATGAAAGCCTCTGAGCTCTTTGGAAGAGAGGACAGGTTCTTGAACCACTTTGCTAACATGCGCTGGTTTGG
CACAGCTGTACCTCTAATTGCA

Alignment

ORF - retro_drer_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.42 %
• Parental protein coverage: 61.32 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAVTLICRPAGVLPKLSGTCSPVLLAAAPVTVQQRKIHHAVVPRGKGGRSSISGLAATVFGATGFLGRY
          MA.VTLICRPAG.LPKLSGTCSPVLLAAAPVTVQQRKIHHAVVP.GKGGRSS.SGLAATVFGATGFLGRY
Retrocopy MASVTLICRPAGILPKLSGTCSPVLLAAAPVTVQQRKIHHAVVPSGKGGRSSFSGLAATVFGATGFLGRY

Parental  VVNRLGRMGSQVVIPYRCDQYDLMYLRPMGDLGQIIFMEWDPRNKESIQRAISHSNVVINLVGREWETSN
          VVNRLGRMGSQVVIPYRCDQYDLMYLRPMGDLGQIIFMEWDPRNKESIQRAISHSNVVINLVGREWETSN
Retrocopy VVNRLGRMGSQVVIPYRCDQYDLMYLRPMGDLGQIIFMEWDPRNKESIQRAISHSNVVINLVGREWETSN

Parental  YKYEDVFVSIPLQIARATREAGIKKFIHMSHLNADIRSPSKYLRNKAVGEEAVRNEFPDAIIMKPSELFG
          YKYEDVFVSIPLQIA.ATREAGIKKFIHMSHLNADIRSPSKYLRNKAVGEEAVRNEFPDAIIMK.SELFG
Retrocopy YKYEDVFVSIPLQIAKATREAGIKKFIHMSHLNADIRSPSKYLRNKAVGEEAVRNEFPDAIIMKASELFG

Parental  REDRFLNHFANMRWFGTAVPLIA
          REDRFLNHFANMRWFGTAVPLIA
Retrocopy REDRFLNHFANMRWFGTAVPLIA

Legend:

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

Expression

RNA-Seq

Danio rerio was not studied using RNA-Seq expression data.

ChIP-Seq

Danio rerio was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_drer_1 retrocopy.

TSS

Danio rerio was not studied using FANTOM5 data.

Lab

retro_drer_1 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_drer_1 has 0 orthologous retrocopies within teleost group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000009588	1 retrocopy	retro_acar_16,
Danio rerio	ENSDARG00000070723	1 retrocopy	retro_drer_1 ,
Homo sapiens	ENSG00000139180	1 retrocopy	retro_hsap_2585,
Gorilla gorilla	ENSGGOG00000006076	1 retrocopy	retro_ggor_1618,
Macaca mulatta	ENSMMUG00000020813	1 retrocopy	retro_mmul_648,
Monodelphis domestica	ENSMODG00000018283	1 retrocopy	retro_mdom_209,
Nomascus leucogenys	ENSNLEG00000003252	1 retrocopy	retro_nleu_1520,
Otolemur garnettii	ENSOGAG00000005225	1 retrocopy	retro_ogar_2244,
Pongo abelii	ENSPPYG00000004171	1 retrocopy	retro_pabe_1905,
Pan troglodytes	ENSPTRG00000004557	1 retrocopy	retro_ptro_1511,
Ictidomys tridecemlineatus	ENSSTOG00000006504	1 retrocopy	retro_itri_543,