RetrogeneDB ID: retro_cjac_1873

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:171789140..171789793(+)
• Located in intron of: ENSCJAG00000018871

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBBP4
• Ensembl ID: ENSCJAG00000001021
• Aliases: None
• Description: retinoblastoma binding protein 4 [Source:HGNC Symbol;Acc:9887]

Sequence

>retro_cjac_1873
TACAAAATATGGAAAAAGAACACTCCTTTTCTTTATGATTTCGTGAATCATAATTCTGGAGTGGCCCAGCCTAACTGCCC
AGTGGCTTCCAGATGTAACCAGACCAGAAGGGAACGATTTCAGCATTCACAACTTGTCCTGGGGACACACACATCGGATG
AACAAAACCATCTTGCTATAGCCAGTGTGCAACTCCCTAATGATGATGCTCAGTTTGATGCGTCACACCATGACAGTGAG
AAAGGAGAATTTGGAGGTTTTGGTTCAGTTAGTGGAAAAACTGAAACAGAAATTAAGAACCATGAAGGAGAAGTAAACAA
GGCTCATTATACGCCCCAGAACCCTTGTATCATCACAACAAAGACTCCTTCCAGTGATGTTCTTGTCTTGGACTATACAA
AACATTTTTCTACGCCAGATCCTTCTGTAGAGTTTAACCCAGACCTGCATCTTCGTGGACATCAGAAGGAAGGCTATGGG
CTTTCTTGGAACCCAAATCTCAGTGGGCACTTGCTTAGTGCTTCGGATGACCACACCATCTGCGTATGGGACAGTACTGT
TCAAAGGAGGGAAAAGTGGTGGATGTGAAGACCATCATTACAGGGCATACAGTGGTAGTAGATGTTTCCTGGCATCTGCT
CCATGAGTCTCTG

Alignment

ORF - retro_cjac_1873 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.89 %
• Parental protein coverage: 52.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  YKIWKKNTPFLYDLVMTH-ALEWPSLTAQWLPDVTRPEGKDFSIH-RLVLGTHTSDEQNHLVIASVQLPN
          YKIWKKNTPFLYD....H..LEWPSLTAQWLPDVTRPEG.DFSIH..LVLGTHTSDEQNHL.IASVQLPN
Retrocopy YKIWKKNTPFLYDF-VNH>ILEWPSLTAQWLPDVTRPEGNDFSIH<QLVLGTHTSDEQNHLAIASVQLPN

Parental  DDAQFDASHYDSEKGEFGGFGSVSGKIEIEIKINHEGEVNRARYMPQNPCIIATKTPSSDVLVFDYTKHP
          DDAQFDASH.DSEKGEFGGFGSVSGK.E.EIK.NHEGEVN.A.Y.PQNPCII.TKTPSSDVLV.DYTKH.
Retrocopy DDAQFDASHHDSEKGEFGGFGSVSGKTETEIK-NHEGEVNKAHYTPQNPCIITTKTPSSDVLVLDYTKHF

Parental  SKPDPSGECNPDLRLRGHQKEGYGLSWNPNLSGHLLSASDDHTICLWDISAVPK-EGKVVDAKTIFTGHT
          S.PDPS.E.NPDL.LRGHQKEGYGLSWNPNLSGHLLSASDDHTIC.WD.S.V...EGKVVD.KTI.TGHT
Retrocopy STPDPSVEFNPDLHLRGHQKEGYGLSWNPNLSGHLLSASDDHTICVWD-STVQR<EGKVVDVKTIITGHT

Parental  AVVEDVSWHLLHESL
          .VV.DVSWHLLHESL
Retrocopy VVV-DVSWHLLHESL

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	1.06 RPM	58.49 RPM
SRP051959_heart	1.00 RPM	50.20 RPM
SRP051959_kidney	1.13 RPM	78.14 RPM
SRP051959_liver	0.48 RPM	56.36 RPM
SRP051959_lung	1.35 RPM	67.14 RPM
SRP051959_lymph_node	1.16 RPM	75.43 RPM
SRP051959_skeletal_muscle	0.63 RPM	44.11 RPM
SRP051959_spleen	1.28 RPM	78.66 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1873 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1873 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1873 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 27 parental genes, and 75 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005904	2 retrocopies	retro_btau_1610, retro_btau_630,
Canis familiaris	ENSCAFG00000010527	1 retrocopy	retro_cfam_1550,
Choloepus hoffmanni	ENSCHOG00000004066	6 retrocopies	retro_chof_1382, retro_chof_1649, retro_chof_1867, retro_chof_2116, retro_chof_2327, retro_chof_908,
Callithrix jacchus	ENSCJAG00000001021	7 retrocopies	retro_cjac_1157, retro_cjac_1787, retro_cjac_1873 , retro_cjac_244, retro_cjac_2557, retro_cjac_2719, retro_cjac_2939,
Cavia porcellus	ENSCPOG00000015352	3 retrocopies	retro_cpor_154, retro_cpor_27, retro_cpor_899,
Equus caballus	ENSECAG00000022784	1 retrocopy	retro_ecab_767,
Echinops telfairi	ENSETEG00000020008	4 retrocopies	retro_etel_1088, retro_etel_1462, retro_etel_1877, retro_etel_676,
Felis catus	ENSFCAG00000027017	1 retrocopy	retro_fcat_1507,
Homo sapiens	ENSG00000162521	6 retrocopies	retro_hsap_1305, retro_hsap_2675, retro_hsap_2814, retro_hsap_3292, retro_hsap_3600, retro_hsap_3601,
Gorilla gorilla	ENSGGOG00000011313	4 retrocopies	retro_ggor_1022, retro_ggor_1314, retro_ggor_1867, retro_ggor_2428,
Macropus eugenii	ENSMEUG00000014379	1 retrocopy	retro_meug_1032,
Myotis lucifugus	ENSMLUG00000000749	2 retrocopies	retro_mluc_2275, retro_mluc_892,
Macaca mulatta	ENSMMUG00000009940	1 retrocopy	retro_mmul_75,
Monodelphis domestica	ENSMODG00000017415	6 retrocopies	retro_mdom_1542, retro_mdom_1833, retro_mdom_1873, retro_mdom_1900, retro_mdom_563, retro_mdom_765,
Mustela putorius furo	ENSMPUG00000015214	1 retrocopy	retro_mputfur_104,
Mus musculus	ENSMUSG00000057236	1 retrocopy	retro_mmus_356,
Nomascus leucogenys	ENSNLEG00000002805	6 retrocopies	retro_nleu_1061, retro_nleu_1179, retro_nleu_1194, retro_nleu_1356, retro_nleu_1379, retro_nleu_2982,
Otolemur garnettii	ENSOGAG00000011632	2 retrocopies	retro_ogar_3079, retro_ogar_3297,
Procavia capensis	ENSPCAG00000011030	1 retrocopy	retro_pcap_116,
Petromyzon marinus	ENSPMAG00000007189	1 retrocopy	retro_pmar_26,
Pongo abelii	ENSPPYG00000001588	6 retrocopies	retro_pabe_1093, retro_pabe_2210, retro_pabe_2720, retro_pabe_2958, retro_pabe_3529, retro_pabe_3611,
Pteropus vampyrus	ENSPVAG00000010981	2 retrocopies	retro_pvam_1094, retro_pvam_902,
Rattus norvegicus	ENSRNOG00000021492	1 retrocopy	retro_rnor_1270,
Sarcophilus harrisii	ENSSHAG00000010923	1 retrocopy	retro_shar_399,
Ictidomys tridecemlineatus	ENSSTOG00000012011	1 retrocopy	retro_itri_1168,
Tupaia belangeri	ENSTBEG00000002236	3 retrocopies	retro_tbel_1360, retro_tbel_1718, retro_tbel_3802,
Vicugna pacos	ENSVPAG00000011876	4 retrocopies	retro_vpac_333, retro_vpac_419, retro_vpac_652, retro_vpac_94,