RetrogeneDB ID: retro_ogar_3402

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873819.1:160734..161554(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AHCY
• Ensembl ID: ENSOGAG00000016787
• Aliases: None
• Description: adenosylhomocysteinase [Source:HGNC Symbol;Acc:343]

Sequence

>retro_ogar_3402
ATTTTGGACAATGGCCTTACCAACCTCATCCACACCAAGTACCCACAGCTCCTGTCAGGCACTCATGGCACCTCTAAGGA
GACCACAACTGTGGTCCACAACCTATACAAGATGATGGCCAGTGGGATCCTGAAAGTACCCACCATCAATGTCAATGACT
CTGTTGACTTTGACGACCTCTATGGTTGTCAGAAGTCCCTCATTGATGGCATCAAATGGGCCACAGATATAATTGTGGGC
AAAGTGGTGGTAGTAGCAGGCTATGGTGATGTAGGCAAGGGCTGTGCCAAGGCTCTGAAGGCTTCTGGGGCCTGTGTCAT
CATCACCAAGATGACACCATCAACACAAGACAGGCTGCCATGGAGAGCTATGAGGTGACCGCCATGGATGAGGCTATCAA
GAGGGCAACATCTTTGTCACCACCACAGGCTGTATTGACATCATTCTCCATTGGCACTTAGAGCAGATGAAGGATGATGC
TGTTGTGTGTAACACTGGACACACTGATGTGGAGACAGATTTTTAGTGCCTTAATGAGAATGCTGTGGAGAAGGTGAACA
TTAAGACCGAGGTGGGCACCTATTTGCTGAAGAACAAGCACACGGTCCTGCTGGCTGAGGGCCGGCCAGTCAACCTAGCG
TGTGCCATGGGCCACCCCAGCTTCGTGTTAAGTAACTCCTTCACCAACTAGGCACTGGCACAGATTGAACTTTGGACTCA
CCCAGACAAGTACCCCATTAGAGTTCACTTCCTATCTAAAAAGCTAGATGACGCAGTGGCTGAAGCTCACGTGGGTAAGC
TGAATGTGAAGCTGACCAAG

Alignment

ORF - retro_ogar_3402 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.43 %
• Parental protein coverage: 65.05 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VLDDGGDLTNLIHTKYPQLLSGEQGGTDGLGAGEGSLLRFILQGYKKKKKKKLSKFIDQSKFDNLYGCRE
          .LD.G..LTNLIHTKYPQLLSG..G...........L......G..K..........D...FD.LYGC..
Retrocopy ILDNG--LTNLIHTKYPQLLSGTHGTSKETTTVVHNLYKMMASGILKVPTINVNDSVD---FDDLYGCQK

Parental  SLIDGIKRATDVMIAGKVAVVAGYGDVGKGCAQALRGFGARVIITEIDP-IIALQAAMEGYEVTTMDEAC
          SLIDGIK.ATD....GKV.VVAGYGDVGKGCA.AL...GA.VIIT...P.I...QAAME.YEVT.MDEA.
Retrocopy SLIDGIKWATDIIV-GKVVVVAGYGDVGKGCAKALKASGACVIITKMTP<INTRQAAMESYEVTAMDEAI

Parental  -QEGNIFVTTTGCTDIILGRHFEQMKDDAVVCNIGHFDVEIDVKWLNENAVKKVNIKPQVDRYFLKNGRR
          .QEGNIFVTTTGC.DIIL..H.EQMKDDAVVCN.GH.DVE.D...LNENAV.KVNIK..V..Y.LKN...
Retrocopy <QEGNIFVTTTGCIDIILHWHLEQMKDDAVVCNTGHTDVETDF*CLNENAVEKVNIKTEVGTYLLKN-KH

Parental  IILLAEGRLVNLGCAMGHPSFVMSNSFTNQVLAQIELWTHPDKYSVGVHFLPKKLDEAVAEAHLGKLNVK
          ..LLAEGR.VNL.CAMGHPSFV.SNSFTN..LAQIELWTHPDKY...VHFL.KKLD.AVAEAH.GKLNVK
Retrocopy TVLLAEGRPVNLACAMGHPSFVLSNSFTN*ALAQIELWTHPDKYPIRVHFLSKKLDDAVAEAHVGKLNVK

Parental  LTK
          LTK
Retrocopy LTK

Legend:

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

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_3402 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii 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 10 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000002576	1 retrocopy	retro_etel_444,
Gorilla gorilla	ENSGGOG00000014694	5 retrocopies	retro_ggor_1148, retro_ggor_1795, retro_ggor_2822, retro_ggor_3087, retro_ggor_511,
Monodelphis domestica	ENSMODG00000002753	1 retrocopy	retro_mdom_1974,
Mus musculus	ENSMUSG00000027597	1 retrocopy	retro_mmus_197,
Nomascus leucogenys	ENSNLEG00000010041	4 retrocopies	retro_nleu_1717, retro_nleu_2785, retro_nleu_40, retro_nleu_929,
Oryctolagus cuniculus	ENSOCUG00000008592	1 retrocopy	retro_ocun_1886,
Otolemur garnettii	ENSOGAG00000016787	3 retrocopies	retro_ogar_3223, retro_ogar_3401, retro_ogar_3402 ,
Rattus norvegicus	ENSRNOG00000017777	7 retrocopies	retro_rnor_1142, retro_rnor_1820, retro_rnor_1903, retro_rnor_2120, retro_rnor_569, retro_rnor_647, retro_rnor_839,
Sus scrofa	ENSSSCG00000007278	1 retrocopy	retro_sscr_119,
Xenopus tropicalis	ENSXETG00000019486	1 retrocopy	retro_xtro_62,