RetrogeneDB ID: | retro_cjac_17 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 5:47192209..47195275(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000000609 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TSHZ1 | ||
| Ensembl ID: | ENSCJAG00000003224 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_17
GCAGGCTACGCCCAGGAGGAACAGCTGAAAGAAGAGGAGGAAATAAAAGAAGAGGAAGAAGAGGACAGTGGTTCAGTAGC
TCAACTGCAGGGTGGCAATGACACAGGGACAGACGAGGACCTAGAAACCGGCCCGGAGCAGAAAGGCTGCTTCAGCTACC
AGAACTCTCCAGGAAGTCATTTGTCCAATCAGGATGCCGAGAACGAGTCTCTGCTGAGCGACGCCAGCGATCAGGTGTCG
GACATCAAGAGCGTCTGCGGCCGAGATGCCTCGGACAAGAAAAGCAACACTCACGTCAAGCTTCCAAACGAAACACACAA
CTGCATGGACAAAATGACTGCGGTCTACGCCAACATCCTGTCTGATTCCTATTGGTCGGGCCTGGGCCTCGGCTTCAAGC
TGTCCAATAGTGAGAGGCGGCACTGTGACACCCGGAATGGCAGCAACAAGAGCGATTTTGATTGGCACCAAGACGCTCTG
TCCAAAAGCCTGCAGCAGAACTTGCCGGCCAGGTCCATCTCGAAACCCAGCCTGTTCAGCTCAGTGCAGCTGTATCGGCA
GAGCAGCAAGATGTGCGGGACTGTGTTCACCGGGGCCAGCCGATTCCGATGCCGGCAGTGCAGCGCTGCCTACGACACCC
TTGTGGAGCTGACCGTGCACATGAACGAAACGGGCCACTATCAAGATGACAACCGCAAGAAGGACAAGCTCAGACCTGCG
AGCTATTCAAAGCCCCGGAAGAGGGCTTTCCAGGATATGGACAAGGAGGATGCTCAGAAGGTTCTGAAATGTATGTTTTG
TGGCGACTCCTTCGATTCCCTCCAAGATTTGAGTGTCCACATGATTAAAACAAAACATTACCAAAAAGTGCCTTTGAAGG
AGCCAGTCCCAACCATTTCCTCGAAGATAGTCACCCCTGCGAAGAAGCGCGTTTTCGATGTCAATCGGCCGTGTTCCCCC
GATTCAACCACAGGATCTTTTGCAGATTCTTTTTCTTCCCAGAAGAACGCCAACTTGCAGTTGTCCTCCAACAACCGCTA
TGGCTACCAGAATGGAGCCAGCTACACCTGGCAGTTTGAGGCCTGCAAGTCCCAGATCTTAAAGTGCATGGAGTGTGGGA
GCTCCCATGACACCTTGCAGCAGCTCACCACCCACATGATGGTCACAGGTCACTTTCTCAAGGTCACCAGCTCTGCCTCC
AAGAAAGGGAAGCAGCTGGTGTTAGACCCGCTGGCTGTAGAGAAAATGCAGTCGTTGTCCGAGGCCCCAAACAGTGATTC
TCTGGCTCCCAAGCCATCCAGTAACTCAGCAGCAGACTGTACAGCCTCTACCACTGAGTTAAAGAAAGAGAGTAAAAAAG
AAAGGCCAGAGGAAACCAGCAAGGATGAGAAAGTCGTGAAAAGCGAGGACTATGAAGATCCTCTACAAAAACCTTTAGAC
CCTACAATCAAATATCAATATCTAAGGGAGGAGGACTTGGAAGATGGCTCAAAGGGTGGTGGGGACATTTTGAAATCTTT
GGAAAATACTGTCACCACAGCCATCAACAAAGCCCAAAATGGGGCCCCCAGCTGGAGTGCCTACCCCAGCATCCACGCAG
CCTATCAGCTGTCCGAGGGCACTAAGCCACCTTTGCCTATGGGATCCCAGGTACTGCAGATCCGGCCTAATCTCACCAAC
AAGCTGAGGCCCATTGCACCAAAGTGGAAAGTGATGCCACTCATTTCTGTGCCCACAAACCTGGCCCCTTACACTCAAGT
CAAGAGGGAGTCAGAAGACAAAGATGAAGTCGTGAAGGAGTGTGGGAAAGAAAGTCCCCATGAAGAGGCCTCATCTTTCA
GCCACAGTGAGGGCGATTCTTTCCGTAAAAGCGAAACGCCCCCAGAAGCCAGAAAGACTGAGCTGGGTCCCCTGAAGGAG
GAGGACAAGCTGATGAAAGAGGGCAGCGAAAAGGAGAAACCCCAGCCGCTGGAGCCCACTTCTGCTCTGAGCAACGGGTG
CGCCCTTGCCAACCACACCCCGGCCCTGCCATGTATCAACCCGCTCAGCGCCCTGCAGTCCGTCCTGAACAATCACCTGG
GCAAAGCCACAGAGCCCTTACGCTCACCTTCCTGCTCCAGCCCAAGTTCAAGCACAATTTCCATGTTCCACAAGTCGAAT
CTCAGTGTCATGGACAAACCAGTCTTGAGTCCCGCCTCCTCAAGGCCAGCTAGCGTATCCAGACGCTACCTGTTTGAGAA
CAACGATCAGCCCATTGACCTGACCAAGTCCAAAAGCAAGAAAGCCGAGTCCTCGCAAGCACAATCCTGTACGTCCCCAC
CTCAGAAGCATGCTCTGTCTGACATCGCAGACATGGTCAAAGTCCTCCCCAAAGCCACCACCCCAAAGCCCGCTGCTTCC
TCCAGGGTCCCTCCCATGAAGCTGGAAATGGACGTTAGGCGCTTTGAGGATGTCTCCAGTGAAGTCTCGACTTTGCATAA
AAGAAAAGGCCGGCAGTCCAACTGGAATCCTCAGCATCTTCTGATTTTACAAGCTCAGTTTGCCTCGAGCCTCTTCCAGA
CATCAGAGGGCAAATACCTGCTGTCCGATCTGGGCCCTCAAGAGCGTATGCAAATCTCGAAGTTTACGGGACTTTCAATG
ACCACTATCAGTCACTGGCTGGCTAACGTCAAGTACCAGCTTAGGAAAACAGGCGGGACAAAATTTCTAAAAAACATGGA
CAAAGGCCACCCCATCTTTTATTGCAGTGACTGTGCCTCCCAGTTCAGAACCCCTTCTACCTACATCAGTCACTTAGAAT
CTCACCTGGGTTTCCAAATGAAGGACATGACCCGCTTGTCAGTGGACCAGCAAAGCAAGGTGGAGCAAGAGATCTCCCGG
GTATCGTCGGCTCAGAGGTCTCCGGAAACAATAGCTGGTGAAGAGGACACAGACTCTAAATTCAAGTGTAAGTTGTGCTG
TCGGACATTTGTGAGCAAACATGCAGTAAAACTCCACCTAAGCAAAACGCACAGCAAGTCACCTGAACACCATTCACAGT
TTGTAACAGACGTGGATGAAGAATAG
ORF - retro_cjac_17 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 50.96 % |
| Parental protein coverage: | 65.61 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | EIKEAQSYQNSPVSSATNQDAGYGSPFSESSDQLAHFKGSSSREEKEDPQCPDSISYPQDS---LAQIKA |
| E.K...SYQNSP.S...NQDA...S..S..SDQ....K....R....D.........P...........A | |
| Retrocopy | EQKGCFSYQNSPGSHLSNQDAENESLLSDASDQVSDIKSVCGRDAS-DKKSNTHVKLPNETHNCMDKMTA |
| Parental | VYANLFSESCWSSLALDLKKSGSTT---STNDASQKSGYDWHQAALAKTLQQTSSYGLLPEPSLFSTVQL |
| VYAN..S.S.WS.L.L..K.S.S......T...S.KS..DWHQ.AL.K.LQQ.........PSLFS.VQL | |
| Retrocopy | VYANILSDSYWSGLGLGFKLSNSERRHCDTRNGSNKSDFDWHQDALSKSLQQNLPARSISKPSLFSSVQL |
| Parental | YRQNNKLYGSVFTGASKFRCKDCSAAYDTLVELTVHMNETGHYRDDNRDKDSEKTKRWSKPRKRSLMEME |
| YRQ..K..G.VFTGAS.FRC..CSAAYDTLVELTVHMNETGHY.DDNR.KD.......SKPRKR....M. | |
| Retrocopy | YRQSSKMCGTVFTGASRFRCRQCSAAYDTLVELTVHMNETGHYQDDNRKKDKLRPASYSKPRKRAFQDMD |
| Parental | GKEDAQKVLKCMYCGHSFESLQDLSVHMIKTKHYQKVPLKEPVPAITKLVPSTKKRALQDLAPPCSPEVA |
| .KEDAQKVLKCM.CG.SF.SLQDLSVHMIKTKHYQKVPLKEPVP.I........K....D...PCSP... | |
| Retrocopy | -KEDAQKVLKCMFCGDSFDSLQDLSVHMIKTKHYQKVPLKEPVPTISSKIVTPAKKRVFDVNRPCSPD-- |
| Parental | GMATEVALSESAKDQKAANPYVTPNNRYGYQNGASYTWQFEARKAQILKCMECGSSHDTLQQLTAHMMVT |
| ...T......S...QK.AN.....NNRYGYQNGASYTWQFEA.K.QILKCMECGSSHDTLQQLT.HMMVT | |
| Retrocopy | --STTGSFADSFSSQKNANLQLSSNNRYGYQNGASYTWQFEACKSQILKCMECGSSHDTLQQLTTHMMVT |
| Parental | GHFLKVTTSASKKGKQLVLDPVVEEKIQSIPLPPTTHTRLLASGIKKQPDSPAGSTASEEKKEPEKEKVP |
| GHFLKVT.SASKKGKQLVLDP...EK.QS....P...............D..A..T..E.KKE..KE... | |
| Retrocopy | GHFLKVTSSASKKGKQLVLDPLAVEKMQSLSEAPNSDSLAPKPSSNSAADCTASTT--ELKKESKKERPE |
| Parental | VAGDTEKI--KEESEDSSEK-FEPSTLYPYLREEDLDDSPKGGVDILKSLENTVSTAISKAQNGAPSWGG |
| .....EK....E..ED...K...P...Y.YLREEDL.D..KGG.DILKSLENTV.TAI.KAQNGAPSW.. | |
| Retrocopy | ETSKDEKVVKSEDYEDPLQKPLDPTIKYQYLREEDLEDGSKGGGDILKSLENTVTTAINKAQNGAPSWSA |
| Parental | YPSIHAAYQL-PGTVKPLPAAVQSVQVQPSYAGGMKSLSSA-EHNALLHSPGSLTPPPHKSNVSAMEELV |
| YPSIHAAYQL..GT..PLP...Q..Q..P.................L...P..L.P.......S.....V | |
| Retrocopy | YPSIHAAYQLSEGTKPPLPMGSQVLQIRPNLTNKLRPIAPKWKVMPLISVPTNLAPYTQVKRESEDKDEV |
| Parental | EKVTGKKEKSSPAKAGSPVAKENKDFPKTE-EVSGKQQKKGHEAESGKAKKEGPLDAHTPNGTEPLKAKV |
| .K..GK...S....A.S....E...F.K.E..........G...E..K..KEG......P...EP..A.. | |
| Retrocopy | VKECGK--ESPHEEASSFSHSEGDSFRKSETPPEARKTELGPLKEEDKLMKEGS-EKEKPQPLEPTSA-L |
| Parental | TNGCSNLGIITDHSPEPSFINPLSALQSIMNTHLGKVSKPV-SPS |
| .NGC........H.P....INPLSALQS..N.HLGK...P..SPS | |
| Retrocopy | SNGCA----LANHTPALPCINPLSALQSVLNNHLGKATEPLRSPS |
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 | 3 .68 RPM | 5 .90 RPM |
| SRP051959_heart | 5 .53 RPM | 8 .23 RPM |
| SRP051959_kidney | 2 .15 RPM | 11 .49 RPM |
| SRP051959_liver | 2 .92 RPM | 3 .55 RPM |
| SRP051959_lung | 7 .09 RPM | 9 .26 RPM |
| SRP051959_lymph_node | 7 .31 RPM | 9 .57 RPM |
| SRP051959_skeletal_muscle | 2 .99 RPM | 5 .50 RPM |
| SRP051959_spleen | 25 .19 RPM | 7 .50 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_17 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_17 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_17 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000003224 | 1 retrocopy |
retro_cjac_17 ,
|
| Ornithorhynchus anatinus | ENSOANG00000001135 | 1 retrocopy |