RetrogeneDB ID: retro_rnor_2120

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 4:247887534..247888559(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ahcy
• Ensembl ID: ENSRNOG00000017777
• Aliases: None
• Description: Adenosylhomocysteinase [Source:UniProtKB/Swiss-Prot;Acc:P10760]

Sequence

>retro_rnor_2120
ATGTCTGATAAACTGCCCTACAAAGTCACGGACATTGGACTAGCTGCCTGGGGATGGAAGGCCCTGGACATAGCTGAGAA
TGAGATGCTGGGTTTGATGAGCATGCGGGAGACATACTCAGCCTCCAAGCCACTGAAGGGCGCTCGCATTGCTGGCTGCC
TGCACATGACTGTGGAGACTGCTGTCCTCATTAAGACTCTCGTGGCTCTGGGTGCTGAGGTGCAGTGGTCCAGCTGCAAC
ATCTTCTCCACTCAGGACCATGCAGCGGCTGCCATTGCCAAGGCTGTCATTCCAGTGTTTGCCTAGAAGGGAGAGATGGA
TAAGAGTATCTGTGGTGCATTGAGCAGACGTTGCACTTCAAGGATGGACCCCTCAACATGATTCTGAACAATGGCGGTGA
CCTTACTAACCTCTTCCACACCAAACACCCACAGCTTCTGTCAAGCATCCGAGGTATCTCTGAGAAAACCACGACTGGCA
TCCACAACCTCTACAAGATGATGGCCAATGGGATACTGAAGGTGCCTGCCATCAACATCAATGATTCTGTCACCAAGAGC
AAGTTTGACAACCTCTATGGCTGCTGGGAGTCCCTCATAGATGGCATCAAACGGACCACAGATGTGATGATTACAGGCAA
GGTGGCAGTGGTAGCAGACCATGGTGATGTGGGCAAGGGTTGTGCCCAGGCCCTGCAGGGTTTCGGGGCCCAAATCATCA
TCACTGAGATTGACCCCATCAATGCACTGCAAGCTGCCATGGAGGGCTATGAGGTAACCACCATGAATGAGGCCTGTAAA
GCAGGCAACATCTTTGTGACCACCACGGGCTGTGTTGATATCGTCCTTGGCCAGCACTTTGAACAGATGAAGGATGATGC
CATTGTCTGTAACATTGGACACTTCGACGTGGAGATTGATGTGAAGTGGCTCAATGAGAACGTCGTGGAGGTGAACATCA
AACCCCAGGTGGACTACTACTTGCTAAAGAATGGGCACCTCATCATCTTGCTGGCTGGAGGCCAA

Alignment

ORF - retro_rnor_2120 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.95 %
• Parental protein coverage: 79.4 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MADKLPYKVADIGLAAWGRKALDIAENEMPGLMRMREMYSASKPLKGARIAGCLHMTVETAVLIETLVAL
          M.DKLPYKV.DIGLAAWG.KALDIAENEM.GLM.MRE.YSASKPLKGARIAGCLHMTVETAVLI.TLVAL
Retrocopy MSDKLPYKVTDIGLAAWGWKALDIAENEMLGLMSMRETYSASKPLKGARIAGCLHMTVETAVLIKTLVAL

Parental  GAEVRWSSCNIFSTQDHAAAAIAKAGIPVFAWKGETDE-EYLWCIEQTLHFKDGPLNMILDDGGDLTNLI
          GAEV.WSSCNIFSTQDHAAAAIAKA.IPVFA.KGE.D..EYLWCIEQTLHFKDGPLNMIL..GGDLTNL.
Retrocopy GAEVQWSSCNIFSTQDHAAAAIAKAVIPVFA*KGEMDK<EYLWCIEQTLHFKDGPLNMILNNGGDLTNLF

Parental  HTKHPQLLSGIRGISEETTTGVHNLYKMMANGILKVPAINVNDSVTKSKFDNLYGCRESLIDGIKRATDV
          HTKHPQLLS.IRGISE.TTTG.HNLYKMMANGILKVPAIN.NDSVTKSKFDNLYGC.ESLIDGIKR.TDV
Retrocopy HTKHPQLLSSIRGISEKTTTGIHNLYKMMANGILKVPAININDSVTKSKFDNLYGCWESLIDGIKRTTDV

Parental  MIAGKVAVVAGYGDVGKGCAQALRGFGARVIITEIDPINALQAAMEGYEVTTMDEACKEGNIFVTTTGCV
          MI.GKVAVVA..GDVGKGCAQAL.GFGA..IITEIDPINALQAAMEGYEVTTM.EACK.GNIFVTTTGCV
Retrocopy MITGKVAVVADHGDVGKGCAQALQGFGAQIIITEIDPINALQAAMEGYEVTTMNEACKAGNIFVTTTGCV

Parental  DIILGRHFEQMKDDAIVCNIGHFDVEIDVKWLNENAVEKVNIKPQVDRYLLKNGHRIILLAEGR
          DI.LG.HFEQMKDDAIVCNIGHFDVEIDVKWLNEN.VE.VNIKPQVD.YLLKNGH.IILLA.G.
Retrocopy DIVLGQHFEQMKDDAIVCNIGHFDVEIDVKWLNENVVE-VNIKPQVDYYLLKNGHLIILLAGGQ

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	0.00 RPM	31.78 RPM
SRP017611_kidney	0.00 RPM	228.82 RPM
SRP017611_liver	0.00 RPM	707.88 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2120 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2120 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2120 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,