RetrogeneDB ID: retro_cjac_1248

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:9013584..9014742(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AHCY
• Ensembl ID: ENSCJAG00000018303
• Aliases: None
• Description: adenosylhomocysteinase [Source:HGNC Symbol;Acc:343]

Sequence

>retro_cjac_1248
TCCAAGCCACTGAAGCGTGCCCACATTGCTGGCTGACCATACATGACCATGGAGACCGCCATCCTCACTGAGACCCTTGT
TGCCCTTGTTGCTGAGGTACAGTGGTTCAGCTGCAACACCTTCTCCACCCAGAATCAGCTGGCAGCTGCCATTGCCCAGG
TTGTCATTCCAGTGCATGCCTGGAAGGGTGAAACAAGCAATGAGTACCTGTGATGCATCCAGCAATCACCATACTTTGAA
GATGTGCCCCTCAACATGATTGTGGATGATGGTGGTAACCTCACCAACCAAATCCACACCAAATACTCACAGCTCTTGCC
AGACATCCAAGGCATCTCTGAAGAGACCACCACCGGGGTCCACAACCTACACAAGATGATGGCCAAAGGAATCCTGAAGG
TGCCTGCTATCAACAACTCCATCACCAAGAGCAAGTTTCACAGCCTCTGAGGCTGCCGGGAGTCACTCATAGATGGCATT
AAGAGGGCCACGGACGTGATAATTGCCAGCAAAGTAGCCATGGTAGCAGTCTATGGCGACATGGGCAAGGACTGTGCCCA
GGCCCTGTGGGGCTTTGGGACCCACTTCATCATCACCAAGATTGGCCCCAGCAACCCACCGCAGGCTGCCATGGAGGGCT
ATGAAGTAACTGCCATAGATGAGGCCTGTTGGGAGGACAACATCTTTGTTACCACCACAGGCTGTGTTGACATCATCCTT
GGCTAGCACTTTGAGCAGATGAAGGATGATGCCATCGTGTGTAACACTGGTCACTTTGACATGGACATTAATGCCAAGTG
GCTCAGTGAGAACGCTGTGAAGGTGACCAAGCCCCAGGTGGCCAGGACTGGCTGAAGAATGGCACAGCACCATTCTGCTG
GTTGAGGGTCGGCTGGTCAGCCTGCATTGTGCCATGGGCCACTCCGGCTTTGGGATGAGTGACCCCTTCACCAACCAGGT
GATGGTGCAGATTGAGCTGTGCCCCACTCAGACAAGTATCCTGGTGGGCTTCACTTGCTGCCCAAGAAGCTGGATGAGGC
AATGGCTGAATCCCACCTGGGCAAGCTGAATGTGAAACTCTCCAAGTTGACCAAGAAGCAGGCCCAGTACCTGGGCGTGC
CCTGTGATGGCCCCTTCAAGCTGGATCATGACCACTAC

Alignment

ORF - retro_cjac_1248 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.59 %
• Parental protein coverage: 90.51 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SKPLMGARIAGCLHMTVETAVLIETLVALGAEVRWSSCNIFSTQDHAAAAIAKAGIPVYAWKGETDEEYL
          SKPL..A.IAG...MT.ETA.L.ETLVAL.AEV.W.SCN.FSTQ...AAAIA...IPV.AWKGET..EYL
Retrocopy SKPLKRAHIAG*PYMTMETAILTETLVALVAEVQWFSCNTFSTQNQLAAAIAQVVIPVHAWKGETSNEYL

Parental  WCIEQTLYFKDGPLNMILDDGGDLTNLIHTKYPQLLPGIRGISEETTTGVHNLYKMMATGVLKVPAINVN
          .CI.Q..YF.D.PLNMI.DDGG.LTN.IHTKY.QLLP.I.GISEETTTGVHNL.KMMA.G.LKVPAIN..
Retrocopy *CIQQSPYFEDVPLNMIVDDGGNLTNQIHTKYSQLLPDIQGISEETTTGVHNLHKMMAKGILKVPAIN--

Parental  DSVTKSKFDNLYGCRESLIDGIKRATDVMIAGKVAVVAGYGDVGKGCAQALRGFGARVIITEIDPINALQ
          .S.TKSKF..L.GCRESLIDGIKRATDV.IA.KVA.VA.YGD.GK.CAQAL.GFG...IIT.I.P.N..Q
Retrocopy NSITKSKFHSL*GCRESLIDGIKRATDVIIASKVAMVAVYGDMGKDCAQALWGFGTHFIITKIGPSNPPQ

Parental  AAMEGYEVTTMDEACQEGNIFVTTTGCVDIILGRHFEQMKDDAIVCNIGHFDVEIDVKWLNENAVEKVNI
          AAMEGYEVT..DEAC.E.NIFVTTTGCVDIILG.HFEQMKDDAIVCN.GHFD..I..KWL.ENAV.....
Retrocopy AAMEGYEVTAIDEACWEDNIFVTTTGCVDIILG*HFEQMKDDAIVCNTGHFDMDINAKWLSENAVKVT--

Parental  KPQVDRYR-LKNG-HRIILLAEGRLVNLGCAMGHPSFVMSNSFTNQVMAQIELW-THPDKYPVGVHFLPK
          KPQV.R...LKNG.H..ILL.EGRLV.L.CAMGH..F.MS..FTNQVM.QIEL...H.DKYP.G.H.LPK
Retrocopy KPQVARTG<LKNG<HSTILLVEGRLVSLHCAMGHSGFGMSDPFTNQVMVQIELC<PHSDKYPGGLHLLPK

Parental  KLDEAVAEAHLGKLNVKLTKLTEKQAQYLGMSRDGPFKPDHYRY
          KLDEA.AE.HLGKLNVKL.KLT.KQAQYLG...DGPFK.DH..Y
Retrocopy KLDEAMAESHLGKLNVKLSKLTKKQAQYLGVPCDGPFKLDHDHY

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
SRP051959_colon	0.00 RPM	6.66 RPM
SRP051959_heart	0.02 RPM	7.79 RPM
SRP051959_kidney	0.00 RPM	49.14 RPM
SRP051959_liver	0.00 RPM	25.54 RPM
SRP051959_lung	0.00 RPM	4.16 RPM
SRP051959_lymph_node	0.00 RPM	3.08 RPM
SRP051959_skeletal_muscle	0.00 RPM	6.38 RPM
SRP051959_spleen	0.00 RPM	5.86 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1248 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1248 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1248 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_1978

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 55 retrocopies.

Species	Parental gene accession	Retrocopies number
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,
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,