RetrogeneDB ID: | retro_cjac_2178 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 3:119324651..119326209(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | XRCC5 | ||
| Ensembl ID: | ENSCJAG00000012291 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_2178
ATGGTGATGATATCTTTAGAAGGTGAAGATGGGTTGGATGAAATTTATTCCTGCAGTGAGAGTCTGAGAAAACTGTGTGT
CTTCAAGAAAATTGAGAGGCATTTCATTCACTAGCCCTACCGACTGACCATTGGCTCCAATTTTTCTATAAGGATTGCAG
CCTATAAATTGATTTTACAGGAGAGAGTTAAAAGGACTTGGACAGTTGTGGATGCAAAAACCCTCAAAAAAGAAGATATA
TAAAAAGAAACAGTTTATTGCTTAAATGATGATGATGAAACCAAAGTTTTAAAAAAGGATATTATTTAAGGGTTCCACTA
TGGATGTGATATACCTTTCTCTAAAGTGGATGAGGAGCAAATGAAATATAAATTGGAGGGAAGTGCTTCTGTTTTGGAAT
TTTGTAAATCTTCTCAGGTTCAGAGAAGATTCTTCATGGGAAATCAAGTTCTAAATGTTTTTGCAGCAAGAGACGAGGCA
GCAGCAGTTGCACTTTCCTCCCTGATTCATGCTTTGGACGAGTTAGACTTGGTGGCCATAGTTTGCTATGCTTATGACAA
AAGAACTAATCCTCAAGTCAGGGTGACTTTTCCTCATATCAAGCATAACCATGAGTGTTTAGTGTATGTGTAGCTGCCTT
TCATGGAAGACTTGCTGCAATATATGTTTTTATCCCTGAAAAACAGTAAGAACTATGCTCCCACCGAGGCATAGTTGAAT
GCTGTTGATATTTTGATTGACTCCATGAGCTTAGTAAAGAAAGATGAGAAGACAGACATCCTTGAAGACTTGTTTCCAAC
CACCCAAATCCCAAATCCTCTATTTCAGAAATTATTTTGGTGTCTGCTGCACAGAGCTTTACATCCCTGGGAGCCTCTAC
CCCCAATTGCAGCATATTTGGAATATGCTGAATCCTCCCACTGAAATAACAGCGAAATGTCAGATTTCTTTCTCTAAAAT
AAAGATCCTTTTTCCTCTGATTGAAGCCAAGAAAAAGGATCAAGTAACTGCTCAGGACATTTTCCAAGACAACCATGAAG
ATGGACTCACCACTAAAAAATTAAAGACTGAGGAAGGGGGAGCCTACTTCCACATCTCCAGCCTGGCTGAAGGCAGTGTC
ACCTCTGCTGGAAGTGTGAATCCTGCTGAAAACTTCCATGTTCTAGTGAAACATAAGAATGCCAGCTTTGAGGAAGCGAG
TGACCAGCTCATAAAACACATCAAACAGTTTTTGGATAATAATGAAACACCGTATTTTATGAAGAGCATGGACTGCATCA
GAGCCTTCCAGGAAGAAGCCATTAAGTTTTCAGAAGATCAGTGCTTTAACAACTTCCTGAAAGCCCTTTGAAAGAAAGTG
GAAATTAAACAATTAAATCCTTTCTGGAAAATTGTTGTTCAGGATGGAATTACTCTGATCACCAAAGAGGAAGCCTCTGG
AAGATCTGTCACAGCTGAGGAAGCCAAAAAGTTTCTGGCCCCTAAAGAAAAACCGAATGAAGACACAGCAGCCATATTTA
AAGAAGGTGGTGATGTAGATGATTTACTGGACATGATA
ORF - retro_cjac_2178 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 79.77 % |
| Parental protein coverage: | 71.45 % |
| Number of stop codons detected: | 6 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MVMISLEGEDGLDEIYSFSESLRKLCVFKKIERHSIHWPCRLTIGSNLSIRIAAYKSILQERVKKTWTVV |
| MVMISLEGEDGLDEIYS.SESLRKLCVFKKIERH.IH.P.RLTIGSN.SIRIAAYK.ILQERVK.TWTVV | |
| Retrocopy | MVMISLEGEDGLDEIYSCSESLRKLCVFKKIERHFIH*PYRLTIGSNFSIRIAAYKLILQERVKRTWTVV |
| Parental | DAKTLKKEDIQKETVYCLNDDDETEILKEDIIQGFRYGSDIVPFSKVDEEQMKYKSEGKCFSVLGFCKSS |
| DAKTLKKEDI.KETVYCLNDDDET..LK.DII.GF.YG.DI.PFSKVDEEQMKYK.EG...SVL.FCKSS | |
| Retrocopy | DAKTLKKEDI*KETVYCLNDDDETKVLKKDII*GFHYGCDI-PFSKVDEEQMKYKLEGSA-SVLEFCKSS |
| Parental | QVQRRFFMGNQVLKVFAARDDEAAAVALSSLIHALNDLDMVAIVRYAYDKRANPQVGVAFPHIKHNYECL |
| QVQRRFFMGNQVL.VFAARD.EAAAVALSSLIHAL..LD.VAIV.YAYDKR.NPQV.V.FPHIKHN.ECL | |
| Retrocopy | QVQRRFFMGNQVLNVFAARD-EAAAVALSSLIHALDELDLVAIVCYAYDKRTNPQVRVTFPHIKHNHECL |
| Parental | VYVQLPFMEDLRQYMFSSLKNSKKYAPTEAQLNAVDALIDSMSLAKKDE-KTNTLEDMFPTTKIPNPRFQ |
| VYV.LPFMEDL.QYMF.SLKNSK.YAPTEA.LNAVD.LIDSMSL.KKDE.....L...F...K.....F. | |
| Retrocopy | VYV*LPFMEDLLQYMFLSLKNSKNYAPTEA*LNAVDILIDSMSLVKKDE>RQTSLKTCFQPPKSQILYFR |
| Parental | RLFQCLLHRALHPREPLPPIQQHIWNMLNPPTEVTKKSQIPLSKIKTLFPLIEAKKKDQVIAQDVFQDNH |
| ..F.........P....P..Q.HIWNMLNPPTE.T.K.QI..SKIK.LFPLIEAKKKDQV.AQD.FQDNH | |
| Retrocopy | NYFGVCCTELYIPGSLYPQLQ-HIWNMLNPPTEITAKCQISFSKIKILFPLIEAKKKDQVTAQDIFQDNH |
| Parental | EDGPTAKKLKTEEGGAHFSISSLAEGSVTSVGSVNPAENFRVLVKQKKASFEEASNQLINHIEQFLDTNE |
| EDG.T.KKLKTEEGGA.F.ISSLAEGSVTS.GSVNPAENF.VLVK.K.ASFEEAS.QLI.HI.QFLD.NE | |
| Retrocopy | EDGLTTKKLKTEEGGAYFHISSLAEGSVTSAGSVNPAENFHVLVKHKNASFEEASDQLIKHIKQFLDNNE |
| Parental | TLYFMKSMDCIRAFREEAIKFSEEQRFNNFLKALREKVESKQLNHFWEIVVQDGITLITKEEASGSSVTA |
| T.YFMKSMDCIRAF.EEAIKFSE.Q.FNNFLKAL..KVE.KQLN.FW.IVVQDGITLITKEEASG.SVTA | |
| Retrocopy | TPYFMKSMDCIRAFQEEAIKFSEDQCFNNFLKAL*KKVEIKQLNPFWKIVVQDGITLITKEEASGRSVTA |
| Parental | EEAKKFLAPKEKPSEDTAAAFEEGGDVEDLLDMI |
| EEAKKFLAPKEKP.EDTAA.F.EGGDV.DLLDMI | |
| Retrocopy | EEAKKFLAPKEKPNEDTAAIFKEGGDVDDLLDMI |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
Expression validation based on RNA-Seq data:
| Library | Retrocopy expression | Parental gene expression |
|---|---|---|
| SRP051959_colon | 0 .00 RPM | 133 .75 RPM |
| SRP051959_heart | 0 .00 RPM | 98 .21 RPM |
| SRP051959_kidney | 0 .02 RPM | 149 .34 RPM |
| SRP051959_liver | 0 .00 RPM | 129 .51 RPM |
| SRP051959_lung | 0 .02 RPM | 120 .05 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 133 .72 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 125 .68 RPM |
| SRP051959_spleen | 0 .00 RPM | 135 .25 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2178 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2178 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2178 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000012291 | 2 retrocopies |
retro_cjac_2178 , retro_cjac_2256,
|