RetrogeneDB ID: | retro_cjac_422 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 1:77035196..77037288(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000035362 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | HEATR2 | ||
| Ensembl ID: | ENSCJAG00000001527 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_422
GTGCTCGCGCCCCACCTGGACGACACCCTTCGCATGCTGCGCTGCTCCCTGCTCGACTCCTTGGCCGCTGTGCACCGCGA
GAGCTGCAGCTGTGCTGCCGTCCTGGCGCAGGCCACGCCCGACCACTTCCACATGCAATCGGAGTCTCTGATCGGTCCCT
GGTGCAGACCATCTCCCACCAGCACTGGAAGGTCCGTGTGGCCGTCATCGAAGCCACGGGCACGATGATCCAGTTTGGCA
ATGGGAAGTCTGTGGACGACGTGCTTTCCCATTTTGCTCAACGGCTGTTTGACGACGTCCCGCAGGTCCGGCGGGCGGTG
GCTTCTGTGGTGGGCGGCTGGCTGCTGCATCTGCGTGACCGCTACTCCTTCTTCCACAAGCTCATACCTTTGCTGCTCAG
CACCCTTGATGACGAGATGCCCGAGGTCAGGCAGCTGGCTGCTAGCCTCTGGGAGGATGTTGGCCTGCAGTGGCAGAGGG
AGAATGAGGAGGAAGGACCTGAAGGACAAGCTGGACTTTGCCCCTCCCTCCCCCACCCCATTACCCTCCGCATGAGCATC
GCCCCGTGCTGGGCTGTCGGAAGCTCTTCTTCAGGAACCTCTCCAAGATCCTCCCCGCATTGTGCCACGACATCACCGAC
TGGGTGGTGGGGACGCGAGTGAAGTCGGTGCAACTGCTGCCCGTGCTGCTGCTGCATGCCGAGGACCACACCACACAACA
CCTGGAGATCGTCCTCCGGACCCTGTTCCTGGCCTGCGCTGACGAGGAGACAGCCGTGGTCCATAGCTGTTCAAGATCCG
CACAGCTCATAGGGACGTTTGTTAACCCTGAGGTATTTCTGAAGCTGATCTTACCAATGCTGAAGAAGGGGCCCTCCGCC
TCCCTCCTCCTGGTGCTGGACTCCACCATTCAGGGCTGCCCCCGAGAAGCCCTCCAGTCGCACCTAACAGCCATTGCCAC
CGAGCTGGCACAGGCCCACATCTGCCAGGCATCTGTAAACGACCTCTACCTGGAGCGTCTGCTGCTCTGCGTGCAGGCCC
TGGTATCCGTGTGTTGCAAGGACTGCGGCATGGCCAGCTTGCAGCTCATGGACGTGCAGCTGACCATAAAGGCCCTCGCA
GGTTCCACCAGCCTCAGGGACAAGGCGCAGGAGACGATGGACTCGCTGGCCGCTGCGGAGGGCGTCAGCAGCTGCCAGAA
CCTCTATCGCAAGTACCTGGGCCCTCTCCTGGAGCGGGCGACCGCGTCGCACCTCGACTGGTCCGCGCCCTCGCCGGAGC
TCCTGTAGTTCAGTGTCATCATCGCGCAGTCGGGCCCCGCCCTAGGAGAAGCCCTGCCGCACGTCATGCACACGCTCAGG
GCCTGTCTGCAGCCCTCCCGAGACCCGCAGATGCGCCTGAAGCTGTTCTCCATCCTGTCCACTATGCTGCCCAGAGCCGC
GGACACCATCGACTCCCATGGGCAGTTACCTAGCTACCTTGAGATGGTGACAAAGGACATCCTGGCCCCCAATCTGCAGT
GGCATGCAGGGAGGACAGCTGCGGCCATCCGCACGGCCGCCGTGTCCTGCCTCTGGGTGCTCACCAGCGGCGAGGTCCTG
TCGGCCAAGCAGATCCAGGACGTGCAGGAAACACTGATGCCTCAAGTCCTGACCACGCTAGAGGAAGATTCGCAGATGAC
TCGGCTGATCTCCTGCCGTATCATCAACACGTTCTTAAAAACCTTGGGCAGCATGATTGATCCAGATAAACTCAAGATTT
ATCCCGAACTCTTAAAGCATCTAGACGACGTTTCCAATGACGTGAGGATGGCAGCTGCCTCCACCCTGGTGACCTGGCTG
CAGTGTGTGAAGAATGTCGATGGAAAGGCCTACTGTCAGAGCAGCGTCCAGTGCCTGTACAGAGAGCTGCTCGTTCACCT
TGACGATCCAGAGAGCGCCATCCAGGACGCCATTTTAGAGGTCCTCAAGGAGGGCAGCGCCCTGTTCCCAGATCTCCTGG
TGAGGGAGACAGAGGCCGTCATCCACAAACACTGCTCGGCCACCTACTGCGAGCAGCTACTGCAGCATGTGCAGACCATG
CCAGCCACGCAG
ORF - retro_cjac_422 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 79.46 % |
| Parental protein coverage: | 88.75 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | IKAPHLDDALRVLRCSLLDPFAAVRRESCSCAAALAQATPDHFHMQSESLIGP-LMQTISHQHWKVRVAA |
| ..APHLDD.LR.LRCSLLD..AAV.RESCSCAA.LAQATPDHFHMQSESLIGP.L.QTISHQHWKVRVA. | |
| Retrocopy | VLAPHLDDTLRMLRCSLLDSLAAVHRESCSCAAVLAQATPDHFHMQSESLIGP<LVQTISHQHWKVRVAV |
| Parental | IEATGTVIQFGNGKSVDDVLSHFAQRLFDDVPQVRRAVASVVGGWLLHLRDRYSFFHKLIPLLLSTIDDE |
| IEATGT.IQFGNGKSVDDVLSHFAQRLFDDVPQVRRAVASVVGGWLLHLRDRYSFFHKLIPLLLST.DDE | |
| Retrocopy | IEATGTMIQFGNGKSVDDVLSHFAQRLFDDVPQVRRAVASVVGGWLLHLRDRYSFFHKLIPLLLSTLDDE |
| Parental | MPEVRQLSASLWEDVGLQWQREN-EE-DLKDKLDFTPP-PPPHYPPHGRCSRHPTLGWDSCIPEFLVSVI |
| MPEVRQL.ASLWEDVGLQWQREN.EE.DLKDKLDF.PP.PPPHYPPH......P.LG........L.... | |
| Retrocopy | MPEVRQLAASLWEDVGLQWQRENEEE>DLKDKLDFAPP>PPPHYPPH---EHRPVLGCRKLFFRNLSKIL |
| Parental | DIWCHGVTCMKLWERSCWYLLLPVCVAHWRHPCLQTLSIILSTETQASEPYKSETVKCCSRSAELIGTFV |
| ...CH..T......R.....LLPV...H......Q.L.I.L.T...A........V..CSRSA.LIGTFV | |
| Retrocopy | PALCHDITDWVVGTRVKSVQLLPVLLLHAEDHTTQHLEIVLRTLFLACADEETAVVHSCSRSAQLIGTFV |
| Parental | NPEVFLKLILPMLKKGPSASGLLVLASTIRGCPREALQPHLKAIATELAQAHICQASENYLFLFILSPEC |
| NPEVFLKLILPMLKKGPSAS.LLVL.STI.GCPREALQ.HL.AIATELAQAHICQAS.N.L.L..L...C | |
| Retrocopy | NPEVFLKLILPMLKKGPSASLLLVLDSTIQGCPREALQSHLTAIATELAQAHICQASVNDLYLERLLL-C |
| Parental | PQKSVSQCRPQRNWAMGKIRDVIRGIIEISESAQRRDKKAQETMDLLATAEGVSSCQDLYRKYMGPLLER |
| .Q..VS.C......A.....DV...I.....S...RDK.AQETMD.LA.AEGVSSCQ.LYRKY.GPLLER | |
| Retrocopy | VQALVSVCCKDCGMASLQLMDVQLTIKALAGSTSLRDK-AQETMDSLAAAEGVSSCQNLYRKYLGPLLER |
| Parental | ATASHLDWTAHSPELLQFSVIIAQSGPALGEALPHIMPTLRACLQPSRDPQMRLKLFSILSTMLLRAADT |
| ATASHLDW.A.SPELL.FSVIIAQSGPALGEALPH.M.TLRACLQPSRDPQMRLKLFSILSTML.RAADT | |
| Retrocopy | ATASHLDWSAPSPELL*FSVIIAQSGPALGEALPHVMHTLRACLQPSRDPQMRLKLFSILSTMLPRAADT |
| Parental | IDSQGQLPSYLEMVTKDILAPNLQWHAGRTAAAIRTAAVSCLWAFTSSEVLSAKQIRDVQETLMPQVLTT |
| IDS.GQLPSYLEMVTKDILAPNLQWHAGRTAAAIRTAAVSCLW..TS.EVLSAKQI.DVQETLMPQVLTT | |
| Retrocopy | IDSHGQLPSYLEMVTKDILAPNLQWHAGRTAAAIRTAAVSCLWVLTSGEVLSAKQIQDVQETLMPQVLTT |
| Parental | LEEDSQMTRLISCRIINTFLKTLGSMIDPDKLIKIYPELLKRLDDVSNDVRMAAASTLVTWLQCVKNADG |
| LEEDSQMTRLISCRIINTFLKTLGSMIDPDKL.KIYPELLK.LDDVSNDVRMAAASTLVTWLQCVKN.DG | |
| Retrocopy | LEEDSQMTRLISCRIINTFLKTLGSMIDPDKL-KIYPELLKHLDDVSNDVRMAAASTLVTWLQCVKNVDG |
| Parental | KAYYQSSIQYLYRELLVHLDDPESAIQDAVLEVLKEGSALFPDLLVRETEAVIHKHRSATYCEQLLQHVQ |
| KAY.QSS.Q.LYRELLVHLDDPESAIQDA.LEVLKEGSALFPDLLVRETEAVIHKH.SATYCEQLLQHVQ | |
| Retrocopy | KAYCQSSVQCLYRELLVHLDDPESAIQDAILEVLKEGSALFPDLLVRETEAVIHKHCSATYCEQLLQHVQ |
| Parental | AVPATQ |
| ..PATQ | |
| Retrocopy | TMPATQ |
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 .44 RPM | 3 .95 RPM |
| SRP051959_heart | 0 .44 RPM | 2 .68 RPM |
| SRP051959_kidney | 0 .64 RPM | 5 .88 RPM |
| SRP051959_liver | 0 .17 RPM | 1 .26 RPM |
| SRP051959_lung | 0 .59 RPM | 4 .31 RPM |
| SRP051959_lymph_node | 0 .34 RPM | 2 .76 RPM |
| SRP051959_skeletal_muscle | 0 .28 RPM | 2 .25 RPM |
| SRP051959_spleen | 0 .19 RPM | 2 .42 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_422 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_422 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_422 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000001527 | 1 retrocopy |
retro_cjac_422 ,
|