RetrogeneDB ID: retro_ocun_1886

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: X:53025862..53027253(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000024906
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: AHCY
• Ensembl ID: ENSOCUG00000008592
• Aliases: None
• Description: adenosylhomocysteinase [Source:HGNC Symbol;Acc:343]

Sequence

>retro_ocun_1886
TCCTGCCCAGCGCCGCCAGCCCAGTGCCTGATTTCTGCTCTAGGCCTGATCCCCTTTTCGCTCGTGTCCATCACCGCGTG
CAGCAATGCCGCCAGAATGTCTGACAAACTGCCCTACAAAGTCGCGGACATTGGCCTGGCTGCGTGGGGACGCAAGGCCC
TGGACATCGCCGAGAACGAGATGCCTGGCCTGATGCGCATGCGGGAGATGTACACGGCCTCCAAGCCACTGAAGGGCGCC
CGCATTGCCGGCTGCCTGCACATGACCGTGGAGACTGCCGTCCTCATTGAGACCCTTGTTGCCCTGGGCGCCAAGGTGCA
GTGGTCCAGCTGCAACATCTTTTCCACCCAGACCACACAGCGGTTGCCATTGCCAAGGCCGGCATTCCAGTGTATGCCTG
GAAGGGCGAAACAGACGAGGAGTACCTGTGGTGCATTGAGCAGACGCTCTACTTTAAGGACGGGCCCCTCAACATGATCC
TGGACGATGGCGGTGACCTCACCAACCTCATACACACCAAGTACCCACAGCTCCTGTCAGGCATCAGGGGCATCTCTGAG
GAGACCATGAGTGGGGTCTACAACCTCTACAAGATGATGGCCAATGGGGTCCTGAAGGTGCCTGCAATCAATGTCAGTGA
CTCCGTCACCAAGAGCAAATTTGACAACCTCTATGGCTGCCGGGAGTCCCTCATCGATGGCATCAAGCGGGCTACAGATG
TGATGATCACAGGCAAGGTGGTGGTGGTTGCAGGCTATGGCGACGTGGGCAGGGGCTGTGCCCAGGCCCTGAGGGGTTTT
GGGGCCCGTGTCATCATCACTGAGATCGACCCCATCAACGCACTGCAGGCTGCCATGGAGGGCTACGAGGTGACCTCCAT
GGATGAAGCCTGCAAGGAGGGCAACATCTTTGTCACTACCACAGGCTGTGTGGACATCATCCTTGGGCGGCACTTTGAGC
AGATGAAGGATGATGCCATCGTGTGTAACATGGGACACTTCAACGTGGAGATTGACGTCAAGTGGCTCAATGAGAATGCA
GTGGAGAAGGTGAACGTCAAGCCCCAGGTGGACCGCTATTGGCTGAAGAATGGGCGCCACATCATCCTGCTTGCCGAGGG
CCGGCTGGTCAATCTGGGCTGTGCCATGGGCCACCCCAGCTTCATGATGAGCAACTCCTTCACAAACCAGGTGCTGGCGC
AGATTGAGCTGTGGACCCACCCTGACAAGTATGCTGTAGGTGTTCACTTCCTGCCCAAGAAGCTGGACGAGGCAGTGGCT
GAAGCCCACCTGAGCAAGCTGAAAGTGAAGCTGACCAAGCTGACTGAGAAGCAGGCCCAGTACCTGGGCATGTCCCGTGA
TGGCCCTTTCAAGCCTGATCACTACCGCTAC

Alignment

ORF - retro_ocun_1886 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.47 %
• Parental protein coverage: 86.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SCPAPPAQCLISALGLIPFSPVCITACSNAARMSDKLPYKVADIGLAAWGRKALDIAENEMPGLMRMREM
          SCPAPPAQCLISALGLIPFS.V.ITACSNAARMSDKLPYKVADIGLAAWGRKALDIAENEMPGLMRMREM
Retrocopy SCPAPPAQCLISALGLIPFSLVSITACSNAARMSDKLPYKVADIGLAAWGRKALDIAENEMPGLMRMREM

Parental  YSASKPLKGARIAGCLHMTVETAVLIETLVALGAEVQWSSCNIFSTQ-DHAAAAIAKAGIPVYAWKGETD
          Y.ASKPLKGARIAGCLHMTVETAVLIETLVALGA.VQWSSCNIFSTQ.DH.A.AIAKAGIPVYAWKGETD
Retrocopy YTASKPLKGARIAGCLHMTVETAVLIETLVALGAKVQWSSCNIFSTQ<DHTAVAIAKAGIPVYAWKGETD

Parental  EEYLWCIEQTLYFKDGPLNMILDDGGDLTNLIHTKYPQLLSGIRGISEETTTGVHNLYKMMANGVLKVPA
          EEYLWCIEQTLYFKDGPLNMILDDGGDLTNLIHTKYPQLLSGIRGISEET..GV.NLYKMMANGVLKVPA
Retrocopy EEYLWCIEQTLYFKDGPLNMILDDGGDLTNLIHTKYPQLLSGIRGISEETMSGVYNLYKMMANGVLKVPA

Parental  INVNDSVTKSKFDNLYGCRESLIDGIKRATDVMIAGKVAVVAGYGDVGKGCAQALRGFGARVIITEIDPI
          INV.DSVTKSKFDNLYGCRESLIDGIKRATDVMI.GKV.VVAGYGDVG.GCAQALRGFGARVIITEIDPI
Retrocopy INVSDSVTKSKFDNLYGCRESLIDGIKRATDVMITGKVVVVAGYGDVGRGCAQALRGFGARVIITEIDPI

Parental  NALQAAMEGYEVTTMDEACKEGNIFVTTTGCVDIILGRHFEQMKDDAIVCNIGHFDVEIDVKWLNENAVE
          NALQAAMEGYEVT.MDEACKEGNIFVTTTGCVDIILGRHFEQMKDDAIVCN.GHF.VEIDVKWLNENAVE
Retrocopy NALQAAMEGYEVTSMDEACKEGNIFVTTTGCVDIILGRHFEQMKDDAIVCNMGHFNVEIDVKWLNENAVE

Parental  KVNIKPQVDRYWLKNGRRIILLAEGRLVNLGCAMGHPSFVMSNSFTNQVLAQIELWTHPDKYAVGVHFLP
          KVN.KPQVDRYWLKNGR.IILLAEGRLVNLGCAMGHPSF.MSNSFTNQVLAQIELWTHPDKYAVGVHFLP
Retrocopy KVNVKPQVDRYWLKNGRHIILLAEGRLVNLGCAMGHPSFMMSNSFTNQVLAQIELWTHPDKYAVGVHFLP

Parental  KKLDEAVAEAHLSKLNVKLTKLTEKQAQYLGMSRDGPFKPDHYRY
          KKLDEAVAEAH...............AQYLGMSRDGPFKPDHYRY
Retrocopy KKLDEAVAEAHXXXXXXXXXXXXXXXAQYLGMSRDGPFKPDHYRY

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.77 RPM	34.55 RPM
SRP017611_kidney	0.30 RPM	160.75 RPM
SRP017611_liver	11.10 RPM	741.69 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1886 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1886 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1886 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 61 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018101	1 retrocopy	retro_btau_1140,
Canis familiaris	ENSCAFG00000007504	2 retrocopies	retro_cfam_1486, retro_cfam_552,
Callithrix jacchus	ENSCJAG00000018303	7 retrocopies	retro_cjac_1028, retro_cjac_1248, retro_cjac_1806, retro_cjac_2132, retro_cjac_2839, retro_cjac_3287, retro_cjac_480,
Echinops telfairi	ENSETEG00000002576	1 retrocopy	retro_etel_444,
Homo sapiens	ENSG00000101444	6 retrocopies	retro_hsap_1496, retro_hsap_2325, retro_hsap_2365, retro_hsap_4213, retro_hsap_571, retro_hsap_803,
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,
Pongo abelii	ENSPPYG00000010935	9 retrocopies	retro_pabe_1247, retro_pabe_1978, retro_pabe_2108, retro_pabe_2189, retro_pabe_3446, retro_pabe_647, retro_pabe_658, retro_pabe_665, retro_pabe_718,
Pan troglodytes	ENSPTRG00000013414	7 retrocopies	retro_ptro_1015, retro_ptro_1698, retro_ptro_1730, retro_ptro_2860, retro_ptro_3011, retro_ptro_559, retro_ptro_771,
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,
Tarsius syrichta	ENSTSYG00000007163	3 retrocopies	retro_tsyr_1178, retro_tsyr_1529, retro_tsyr_1582,
Tursiops truncatus	ENSTTRG00000003632	1 retrocopy	retro_ttru_1666,
Xenopus tropicalis	ENSXETG00000019486	1 retrocopy	retro_xtro_62,