RetrogeneDB ID: retro_ogar_3223

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873745.1:492793..493844(-)
• Located in intron of: ENSOGAG00000008813

Retrocopy information

• Ensembl ID: ENSOGAG00000025414
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_ogar_3223
TTGAGGGGGCGCCTGCACATGACTGCAGAGATCACCATCTTCATTGAGACCCTCATCACCCTGGGTGCTGAGGTACAGTG
GTCTGGCTGCAACATCTTCTTTACCCAGGACCATGCAGCAGCTGCCACTGCCAAGACTGGAATTCCAATGTTCGCCTGGA
AGGGTGAGATGGACAAGGAGTACTTGTGGTGTATCAAGCAGATGCTGTACTTTAAGGTCAAGATGATTTTGGACGATGGT
GGTGACCTTACCAACCTTATCCACACCGAGTACCCGCAGTTTCTCTCAGGCATCTGCAGTATCTCTAAGGAGACCACAAC
TGGGGTCCACAACCTATACAAGATGATGGCCAGTGGGATCCTGAAAGTGCCCGCCATCAATGTCAATGACTCTGTCATCA
AGAGCGAGTTTGACAACTTTTATGGTTGCCCAAAGTCCCTTACTGATGGCATCAAATGGGCCACAGATATGAATGCAAGC
AAGGTGGCAATAGCAGGCTATGGTGATGTAGGCAAGGGCTGTGCCCAGGTTCTGAGGGGTTTTGGGGCCTGCGTCACCAT
CACTGAGATTGACACCATCAACACATTACAGGCTGCCATGAAGGGCTATGAAGTGACCACTATGGATGAGGGCAACATCT
TTTGTCACCACCACAGGCTGTACTGACATCATTCTCAGTTGGCATTTGGCGCAAATGAAGGATGATGCTGTCTTGTGTAA
TACTCGACACTCTGACGTGGAGACAGATGTCAAGTGGCTTAATAAGAATGCTATGGAGAAGGTGAACATTAAGCCCCAAG
TGGGCCTCTATTTGCTGAAGAATGAGCACCACATAATCCTGCTGGCTGAGGGCTGGCTGATCAACCCAGGCTGCGCCATG
GGCCACCCTAGCTTTGTGATGAGTAACTCCTTAACCAACCAGGCGCTAGCAGAGATTGAACTTTGGACTCACCCAGGCAA
GTACCCCATCAGGGTTCACTTCCTGCCTAAAAAGCTGGATGAGGCAGTGGCTGAAGCCCATCTGGGTAAGCTGAACGTGA
AGCTGACCAAG

Alignment

ORF - retro_ogar_3223 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.17 %
• Parental protein coverage: 83.1 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IAGCLHMTVETAVLIETLIALGAEVQWSSCNIFSTQDHAAAAIAKAGIPVYAWKGETDEEYLWCIEQTLY
          ..G.LHMT.E....IETLI.LGAEVQWS.CNIF.TQDHAAAA.AK.GIP..AWKGE.D.EYLWCI.Q.LY
Retrocopy LRGRLHMTAEITIFIETLITLGAEVQWSGCNIFFTQDHAAAATAKTGIPMFAWKGEMDKEYLWCIKQMLY

Parental  FKDGPLNMVLDDGGDLTNLIHTKYPQLLSGEQGGTDGLGAGEGSLLRFILQGYKKKKKKKLSKFIDQSKF
          FK.....M.LDDGGDLTNLIHT.YPQ.LSG..........G...L......G..K............S.F
Retrocopy FK---VKMILDDGGDLTNLIHTEYPQFLSGICSISKETTTGVHNLYKMMASGILKVPAINVNDSVIKSEF

Parental  DNLYGCRESLIDGIKRATDVMIAGKVAVVAGYGDVGKGCAQALRGFGARVIITEIDPIIALQAAMEGYEV
          DN.YGC..SL.DGIK.ATD.M.A.KVA..AGYGDVGKGCAQ.LRGFGA.V.ITEID.I..LQAAM.GYEV
Retrocopy DNFYGCPKSLTDGIKWATD-MNASKVAI-AGYGDVGKGCAQVLRGFGACVTITEIDTINTLQAAMKGYEV

Parental  TTMDEACQEGNIF-VTTTGCTDIILGRHFEQMKDDAVVCNIGHFDVEIDVKWLNENAVKKVNIKPQVDRY
          TTMD....EGNIF.VTTTGCTDIIL..H..QMKDDAV.CN..H.DVE.DVKWLN.NA..KVNIKPQV..Y
Retrocopy TTMD----EGNIF>VTTTGCTDIILSWHLAQMKDDAVLCNTRHSDVETDVKWLNKNAMEKVNIKPQVGLY

Parental  FLKNGRRIILLAEGRLVNLGCAMGHPSFVMSNSFTNQVLAQIELWTHPDKYSVGVHFLPKKLDEAVAEAH
          .LKN...IILLAEG.L.N.GCAMGHPSFVMSNS.TNQ.LA.IELWTHP.KY...VHFLPKKLDEAVAEAH
Retrocopy LLKNEHHIILLAEGWLINPGCAMGHPSFVMSNSLTNQALAEIELWTHPGKYPIRVHFLPKKLDEAVAEAH

Parental  LGKLNVKLTK
          LGKLNVKLTK
Retrocopy LGKLNVKLTK

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_3223 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.

---

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,