RetrogeneDB ID: retro_cjac_2385

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:144172198..144173071(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VDAC2
• Ensembl ID: ENSCJAG00000001145
• Aliases: None
• Description: voltage-dependent anion channel 2 [Source:HGNC Symbol;Acc:12672]

Sequence

>retro_cjac_2385
GGCATTGTCTCTGAGAAGAAGATTGCTGTGCCACCCATATATGCTAATCTTGGCAAATCTGCCAAGCATGTCTTTACCAA
GGTGTATGGATTTGGCTTAATATAACCTGATTTGAAACAAAATCTGAAAATGGATTGGAATTTACAAGCTCAGGCTCAGC
CAACACTGAGACCACCAAAGTGACAGGCAGTCTGGAAAGCAAGTACAGATGTACCAAATATGGCCTGACATTTAGGAAGA
AATGGAACACTGACAATACCCTACACACCAAGATTACTATGGAAGATCAGCTTGCACTTGGACTGAAGCTGACCTTCCGT
TCATCCTTCTCCCCTAACACTTGGGGAAAAAAATGCTAAAATCAAGACAGGCTGCAAGTGGGAGCATATTTTAACCTGGG
CTACGACGTGGATTTGAACATGGCTAGGCCTTCAGCCTGAAGCGCTCTAAGTGCTGGGTTATGAGAGTTGGCTGGCCAGC
TATCAGGTGAATTTTGAGACCACAAAGTTCTGAGTGACCCAGAGTAACTTTGTGGTTGGCTACAAAACTGATGAATTCCA
ACCTCACACTAATGTGAATGGAGGGACAGAGTTTGGCGGCTCCATTTACCAGAAGCTGAGCAAGAAGTTGGAGACTGCTG
TCAGTCTCGCTGGGACAGTAGGAAACAGTAACACTCACTTTGGAATAGCAGCCAAGTATCAGATCGGCCTTGAAGCCCAT
TTCTCCACTAAAATAACAACTCCAGCCCGATAGGTTTAGGATACACTCAAACCCTAAAGCCAGGTATCAGCTGACACTGT
CAGTTTCTCCTGGGTGGCAAGAACGTCAAGTGCTGATGGTCACAAGGTTTGTCTAGGACTGGAATTTCAAGCA

Alignment

ORF - retro_cjac_2385 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.56 %
• Parental protein coverage: 98.64 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GQTCARPMCIPPSYADLGKAARDIFNKGFGFGLVKLDVK-TKSCSGVEFSTSGSSNTDTGKVTGTLETKY
          G.........PP.YA.LGK.A...F.K..GFGL...D.K.TKS..G.EF..SGS.NT.T.KVTG.LE.KY
Retrocopy GIVSEKKIAVPPIYANLGKSAKHVFTKVYGFGLI*PDLK<TKSENGLEFTSSGSANTETTKVTGSLESKY

Parental  KWCEYGLTFTEKWNTDNTLGTEIAIEDQICQGLKLTFDTTFSPNT-GKKSGKIKSSYKRECINLGCDVDF
          ....YGLTF..KWNTDNTL.T.I..EDQ...GLKLTF...FSPNT.GKK.............NLG.DVD.
Retrocopy RCTKYGLTFRKKWNTDNTLHTKITMEDQLALGLKLTFRSSFSPNTWGKKC*NQDRLQVGAYFNLGYDVDL

Parental  DFAGPAIHGSA-VFGYEGWLAGYQMTFDSAKSKLTRSNFAVGYRTGDFQLHTNVNDGTEFGGSIYQKVCE
          ..A.P.......V.GYE.WLA.YQ..F...K...T.SNF.VGY.T..FQ.HTNVN.GTEFGGSIYQK...
Retrocopy NMARPSA*SAL>VLGYESWLASYQVNFETTKF*VTQSNFVVGYKTDEFQPHTNVNGGTEFGGSIYQKLSK

Parental  GLDTSVNLAWTSGTNCTRFGIAAKYQLDPTASISAKV-NNSSLIGVGYTQTLRPGVKLTLSALVDGKSI-
          .L.T.V.LA.T.G...T.FGIAAKYQ....A..S.K..NNSS.IG.GYTQTL.PG.......L..GK...
Retrocopy KLETAVSLAGTVGNSNTHFGIAAKYQIGLEAHFSTKI<NNSSPIGLGYTQTLKPGIS*HCQFLLGGKNV>

Parental  NAGGHKLGLALELEA
          .A.GHK..L.LE..A
Retrocopy SADGHKVCLGLEFQA

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	0.69 RPM	49.61 RPM
SRP051959_heart	0.86 RPM	81.67 RPM
SRP051959_kidney	0.64 RPM	65.78 RPM
SRP051959_liver	0.45 RPM	47.11 RPM
SRP051959_lung	0.88 RPM	30.94 RPM
SRP051959_lymph_node	0.71 RPM	32.14 RPM
SRP051959_skeletal_muscle	0.15 RPM	120.00 RPM
SRP051959_spleen	1.18 RPM	34.58 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2385 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2385 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2385 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012975	2 retrocopies	retro_btau_1252, retro_btau_1389,
Canis familiaris	ENSCAFG00000015398	1 retrocopy	retro_cfam_376,
Callithrix jacchus	ENSCJAG00000001145	1 retrocopy	retro_cjac_2385 ,
Callithrix jacchus	ENSCJAG00000013556	8 retrocopies	retro_cjac_1216, retro_cjac_1669, retro_cjac_1728, retro_cjac_2677, retro_cjac_3183, retro_cjac_3864, retro_cjac_454, retro_cjac_907,
Felis catus	ENSFCAG00000026943	3 retrocopies	retro_fcat_1385, retro_fcat_804, retro_fcat_815,
Homo sapiens	ENSG00000165637	1 retrocopy	retro_hsap_2114,
Gorilla gorilla	ENSGGOG00000005861	5 retrocopies	retro_ggor_1677, retro_ggor_1949, retro_ggor_2934, retro_ggor_3036, retro_ggor_425,
Macropus eugenii	ENSMEUG00000012995	1 retrocopy	retro_meug_30,
Myotis lucifugus	ENSMLUG00000007500	2 retrocopies	retro_mluc_1710, retro_mluc_2252,
Mustela putorius furo	ENSMPUG00000003268	1 retrocopy	retro_mputfur_354,
Mus musculus	ENSMUSG00000021771	1 retrocopy	retro_mmus_2667,
Otolemur garnettii	ENSOGAG00000030039	1 retrocopy	retro_ogar_2116,
Rattus norvegicus	ENSRNOG00000013505	1 retrocopy	retro_rnor_2652,
Sarcophilus harrisii	ENSSHAG00000012048	1 retrocopy	retro_shar_325,
Tupaia belangeri	ENSTBEG00000001946	4 retrocopies	retro_tbel_1504, retro_tbel_1541, retro_tbel_1885, retro_tbel_4597,
Tarsius syrichta	ENSTSYG00000004764	1 retrocopy	retro_tsyr_14,
Vicugna pacos	ENSVPAG00000008068	1 retrocopy	retro_vpac_156,