RetrogeneDB ID: retro_cjac_41

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 16:45392269..45394180(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000018953
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000015833
• Aliases: None
• Description: None

Sequence

>retro_cjac_41
ATGAACCCCAGCACCCCCAGCTACCCCATGGCTTCGCTCTACGTGGGGGACCTCCACCCCTACGTGACCGAGGCGATGCT
CTTCGAGAAGTTCAGCCCGGCCGGGCCCATCCTTTCCATCCGGGTCTGCAGGGACATGATCACCCACCGCTCCTTGGGCT
ACGCGTACGTGAACTTCCAGCAGCCGGCTGACGCCGAGCGTGCTTTGGACACCATGAATTTTGATGTTATAAAGGGCAAG
CCAGTACGCATCATGTGGTCTCAGCGTGATCCATCACTTCGAAAAAGTGGAGTGGGCAACATATTCATTAAAAATCTGGA
CAAATCCATTGATAATAAAGCATTGTATAATATATTTTCTGCTTTTGGTACCATCCTTTCATGTAAGGTGGTTTGTGATG
AAAATGGTCCCAAGGGCTATGGATTTGTACACTTTGAGACACAGGAAGCCGCTGAAAGAGCTATTGAAAAAATGAATGGA
ATGCTCCTAAATGATCGCAAAGTATTTGTTGGACCATTTAAGTCCCGTAAAGAAAGAGAAGCTGAACTTGGAGCTAGGGC
AAAAGAGTTCACCAATGTTTACATCAAGAATTTTGGAGAAGACATGGATGACGAGCACCTTAAGGATCTCTTTGGCAAGT
TTGGGCCTGCCTTAAGTGTGAAAGTAATGACTGATGAAAGTGGAAAATCCAAAGGATTTGGATTTGTAAGCTTTGAAAGG
CATGAAGATGCACAGAAAGCTGTGGATGTGATGAATGGAAAGGAGCTCAATGGAAAACAAATTTATGTTGGTCGAGCTCA
GAAAAAGGTGGAACGGCAGACGGAACTTAAACGCAAATTTGAACAGATGAAGCAAGATAGGATCACCAGATACCAGGGTG
TTAATCTTTACGTGAAAAATCTTGATGATGGTATTGATGATGAACGTCTCCGTAAAGAGTTTTCTCCATTTGGTACAATC
ACTAGTGCAAAGGTTATGATGGAGGGTGGTCGCAGCAAAGGGTTTGGTTTTGTATGTTTCTCCTCCCCAGAAGAAGCTAC
TAAAGCTGTTACAGAAATGAACGGTAGAATTGTGGCCACAAAGCCATTGTATGTAGCTTTAGCTCAGCGCAAAGAAGAGC
GCCAGGCTCACCTCACTAACCTGTATATGCAGAGAATGGCAAGTGTACGAGCTGTGCCCAACCCTCTAATCAACCCCTAC
CAGCCAGCACCTCCTTCAGCTTACTTCATGGCAGCTATCCCACAGACTCAGAACCGTGCTGCATACTATCCTCCTAGACA
AATTGCTCAACTAAGACCAAGTCCTCGCTGGACTGCTCAGGGTGCCAGACCTCATCCATTCCAAAATATGCCTGGTGCTA
TCCACCCAGCTGCTCCTAGACCACCATTTAGTACTATGAGACCAGCTTCTTCACAGGTTCCACGAGTCATGTCAACACAG
CGTGTTGCTGACACATCAACACAGACAAAGGGTCCACGTCCTGCAGCTGCAGCTGCTGCAGCTACTCCTGCTGTCCGCAC
CGTTCCACAGTATAAATATGCTGTGGGAGTTCGCAATCCTCAGCAACATCTTAATGCACAGCCACAAGTTACAATGCAAC
AGCCTGCTGTTCATGTACAAGGTCAAGAACCTTTGACTGCTTCCATGTTGGCATCTGCCCCTCCTCAAGAGCAAAAGCAA
ATGTTGGGTGAATGGCTGTTTCCTCTTATTCAAGCCATGCACCCTTCTCTTGCTGGTAAAATCACTGGTATGTTGTTGGA
GATTGATAATTCAGAACTTCTTCATATCCTTGAGTCTCCAGAGTCACTCCGTTCTAAGGTTGATGAAGCTGTAGCTGTAC
TACAGGCCCACCAAGCTAAAGAGGCTGCCCAGAAAGCCGCTAACAGTGCCACCGGTGTTCCAGCTGTTTAA

Alignment

ORF - retro_cjac_41 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.38 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD
          MNPS.PSYPMASLYVGDLHP.VTEAML.EKFSPAGPILSIRVCRDMIT.RSLGYAYVNFQQPADAERALD
Retrocopy MNPSTPSYPMASLYVGDLHPYVTEAMLFEKFSPAGPILSIRVCRDMITHRSLGYAYVNFQQPADAERALD

Parental  TMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGY
          TMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALY..FSAFG.ILSCKVVCDENG.KGY
Retrocopy TMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYNIFSAFGTILSCKVVCDENGPKGY

Parental  GFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGEDMDDERLKDL
          GFVHFETQEAAERAIEKMNGMLLNDRKVFVG.FKSRKEREAELGARAKEFTNVYIKNFGEDMDDE.LKDL
Retrocopy GFVHFETQEAAERAIEKMNGMLLNDRKVFVGPFKSRKEREAELGARAKEFTNVYIKNFGEDMDDEHLKDL

Parental  FGKFGPALSVKVMTDESGKSKGFGFVSFERHEDAQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKRKF
          FGKFGPALSVKVMTDESGKSKGFGFVSFERHEDAQKAVD.MNGKELNGKQIYVGRAQKKVERQTELKRKF
Retrocopy FGKFGPALSVKVMTDESGKSKGFGFVSFERHEDAQKAVDVMNGKELNGKQIYVGRAQKKVERQTELKRKF

Parental  EQMKQDRITRYQGVNLYVKNLDDGIDDERLRKEFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAV
          EQMKQDRITRYQGVNLYVKNLDDGIDDERLRKEFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAV
Retrocopy EQMKQDRITRYQGVNLYVKNLDDGIDDERLRKEFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAV

Parental  TEMNGRIVATKPLYVALAQRKEERQAHLTNQYMQRMASVRAVPNPVINPYQPAPPSGYFMAAIPQTQNRA
          TEMNGRIVATKPLYVALAQRKEERQAHLTN.YMQRMASVRAVPNP.INPYQPAPPS.YFMAAIPQTQNRA
Retrocopy TEMNGRIVATKPLYVALAQRKEERQAHLTNLYMQRMASVRAVPNPLINPYQPAPPSAYFMAAIPQTQNRA

Parental  AYYPPSQIAQLRPSPRWTAQGARPHPFQNMPGAIRPAAPRPPFSTMRPASSQVPRVMSTQRVANTSTQTM
          AYYPP.QIAQLRPSPRWTAQGARPHPFQNMPGAI.PAAPRPPFSTMRPASSQVPRVMSTQRVA.TSTQT.
Retrocopy AYYPPRQIAQLRPSPRWTAQGARPHPFQNMPGAIHPAAPRPPFSTMRPASSQVPRVMSTQRVADTSTQTK

Parental  GPRPAAAAAAATPAVRTVPQYKYAAGVRNPQQHLNAQPQVTMQQPAVHVQGQEPLTASMLASAPPQEQKQ
          GPRPAAAAAAATPAVRTVPQYKYA.GVRNPQQHLNAQPQVTMQQPAVHVQGQEPLTASMLASAPPQEQKQ
Retrocopy GPRPAAAAAAATPAVRTVPQYKYAVGVRNPQQHLNAQPQVTMQQPAVHVQGQEPLTASMLASAPPQEQKQ

Parental  MLGERLFPLIQAMHPSLAGKITGMLLEIDNSELLHMLESPESLRSKVDEAVAVLQAHQAKEAAQKAVNSA
          MLGE.LFPLIQAMHPSLAGKITGMLLEIDNSELLH.LESPESLRSKVDEAVAVLQAHQAKEAAQKA.NSA
Retrocopy MLGEWLFPLIQAMHPSLAGKITGMLLEIDNSELLHILESPESLRSKVDEAVAVLQAHQAKEAAQKAANSA

Parental  TGVPTV
          TGVP.V
Retrocopy TGVPAV

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	0.09 RPM	64.39 RPM
SRP051959_heart	0.12 RPM	55.83 RPM
SRP051959_kidney	0.13 RPM	49.21 RPM
SRP051959_liver	0.19 RPM	70.90 RPM
SRP051959_lung	0.41 RPM	87.34 RPM
SRP051959_lymph_node	0.16 RPM	84.11 RPM
SRP051959_skeletal_muscle	0.02 RPM	31.93 RPM
SRP051959_spleen	0.25 RPM	123.49 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

2 EST(s) were mapped to retro_cjac_41 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
HX591940	45392207	45393053	99.6	842	4	838
HX623210	45392229	45393002	99.5	769	4	765

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_41 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_41 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 26 parental genes, and 52 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000348	1 retrocopy	retro_amel_1650,
Choloepus hoffmanni	ENSCHOG00000008178	1 retrocopy	retro_chof_2531,
Callithrix jacchus	ENSCJAG00000002512	3 retrocopies	retro_cjac_214, retro_cjac_2722, retro_cjac_284,
Callithrix jacchus	ENSCJAG00000010803	1 retrocopy	retro_cjac_1022,
Callithrix jacchus	ENSCJAG00000014861	1 retrocopy	retro_cjac_1040,
Callithrix jacchus	ENSCJAG00000015833	5 retrocopies	retro_cjac_1586, retro_cjac_2571, retro_cjac_3218, retro_cjac_4039, retro_cjac_41 ,
Cavia porcellus	ENSCPOG00000012917	1 retrocopy	retro_cpor_1324,
Dasypus novemcinctus	ENSDNOG00000008718	2 retrocopies	retro_dnov_1530, retro_dnov_2259,
Felis catus	ENSFCAG00000001874	1 retrocopy	retro_fcat_1927,
Homo sapiens	ENSG00000070756	1 retrocopy	retro_hsap_88,
Gorilla gorilla	ENSGGOG00000006785	1 retrocopy	retro_ggor_1986,
Myotis lucifugus	ENSMLUG00000012245	1 retrocopy	retro_mluc_579,
Macaca mulatta	ENSMMUG00000017786	2 retrocopies	retro_mmul_1462, retro_mmul_895,
Monodelphis domestica	ENSMODG00000006222	4 retrocopies	retro_mdom_123, retro_mdom_1867, retro_mdom_216, retro_mdom_43,
Mus musculus	ENSMUSG00000022283	2 retrocopies	retro_mmus_102, retro_mmus_2164,
Nomascus leucogenys	ENSNLEG00000003142	3 retrocopies	retro_nleu_221, retro_nleu_2412, retro_nleu_611,
Oryctolagus cuniculus	ENSOCUG00000004354	1 retrocopy	retro_ocun_13,
Pongo abelii	ENSPPYG00000018790	3 retrocopies	retro_pabe_2373, retro_pabe_68, retro_pabe_854,
Pteropus vampyrus	ENSPVAG00000016640	2 retrocopies	retro_pvam_10, retro_pvam_855,
Rattus norvegicus	ENSRNOG00000008639	3 retrocopies	retro_rnor_1228, retro_rnor_2321, retro_rnor_265,
Sarcophilus harrisii	ENSSHAG00000011267	1 retrocopy	retro_shar_24,
Sus scrofa	ENSSSCG00000006063	2 retrocopies	retro_sscr_1153, retro_sscr_1205,
Ictidomys tridecemlineatus	ENSSTOG00000016395	2 retrocopies	retro_itri_139, retro_itri_48,
Tarsius syrichta	ENSTSYG00000004229	2 retrocopies	retro_tsyr_1743, retro_tsyr_273,
Tursiops truncatus	ENSTTRG00000004689	2 retrocopies	retro_ttru_1050, retro_ttru_1812,
Vicugna pacos	ENSVPAG00000003865	4 retrocopies	retro_vpac_14, retro_vpac_384, retro_vpac_620, retro_vpac_649,