RetrogeneDB ID: | retro_cjac_3821 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | GL284785.1:9435..10551(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | MAEA | ||
| Ensembl ID: | ENSCJAG00000001587 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_3821
AAGGTGCCCTACGAGACAGTGAACAAACGCTTTCACGCCGCTCAGAAGAACACTGACAAGGAGACCAGCCACGTCACTAT
GGTGGTGGCCGAGCTGGAGAAGACGCTGAGTGTCTGCCCCGCCGTGGACTCTGTGGTCAGCCTGCTGGACGGTGTGGTGG
AGAAGCTCAGCATCCTTAAGAGGAAGGCGGCGGAGTCCATCCAGGCAGAGGATGAGAGCGCCAAGCTGTGCGAGAGCCGG
ATCGAGCACCTCAAAGAGCACAGCAGCGACCAGCCCTCGGTGTCCAGCGTGTGGAAGAGCAAGGACATGGACCGCATGGT
GGGGGAGCACCTGCTAAGCTGCGGCTACTACAACACGGCTGTCAAACTGGCACGCCAGAGCGGCATCAAGGACCTCGTGA
ATATCGAGATGTTCCTGACGGCCAAAGAGGTAGAGGAGTCCCTGGAGCGATGTGAGACAGCCACCTGCCTGGCCTGGTGC
CATGACAAGTCCTGGCTCTGGAAGATGAAGAGCTGCCTGGAGTTCAGCCTCAGAATCCAGGAGTTCATTGAACTCATCCG
GCAGAATAAGAGACTGGATGCCGTTAGACATGCGAGAAAGCACTTCACCCAAGTGGAAGGGAGCTAGCTGGACGAGGTGC
GCCAGGCCATGGGCATGCTGGCCTTCCTCCCTGACACGCACGTCTCCCCGTACAAGGACCTCCGGGACCCCGCACGGTGG
CGGATACTGATCCAGCAGTTCCGGTATGACAATACCGACTACACCAGCTGGGAAACAACTCCGTGTTCACCCTCACCCTG
CAGGCTGGCCTCTCCGCCATCAAGACACCACAGTACTACAAGGAGGACGGCAGCTCCAAGAGCCCCGACTGCCGTGTGCA
GCCGCTCCCTCAACAAGCTGGCGCAGCCCCTGCCCATGGCCCACTGCGCCAACTCCCGCCTGGACTACAAGATCTCCGGT
GATGTGATGAACCACAACAACCTGCCCATGATGCTGCCCAACGGCTACGTCTACGGCTACAATTCTCTGCTTTCTATCCG
TCAAGATGATAAAGTCATTTGCCCGAGAACCAAAGAAGTCTTTCACTTCTCATAAGCCGAGAAGGTGTACATCATG
ORF - retro_cjac_3821 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 76.46 % |
| Parental protein coverage: | 99.73 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | QVPYETLNKRFRAAQKNIDRETSHVTMVVAELEKTLSGCPAVDSVVSLLDGVVEKLSVLKRKAVESIQAE |
| .VPYET.NKRF.AAQKN.D.ETSHVTMVVAELEKTLS.CPAVDSVVSLLDGVVEKLS.LKRKA.ESIQAE | |
| Retrocopy | KVPYETVNKRFHAAQKNTDKETSHVTMVVAELEKTLSVCPAVDSVVSLLDGVVEKLSILKRKAAESIQAE |
| Parental | DESAKLCKRRIEHLKEHSSDQPAAASVWKRKRMDRMMVEHLLRCGYYNTAVKLARQSGIEDLVNIEMFLT |
| DESAKLC..RIEHLKEHSSDQP...SVWK.K.MDRM..EHLL.CGYYNTAVKLARQSGI.DLVNIEMFLT | |
| Retrocopy | DESAKLCESRIEHLKEHSSDQPSVSSVWKSKDMDRMVGEHLLSCGYYNTAVKLARQSGIKDLVNIEMFLT |
| Parental | AKEVEESLERRETATCLAWCHDNKSRLRKMKSCLEFSLRIQEFIELIRQNKRLDAVRHARKHFSQAEGSQ |
| AKEVEESLER.ETATCLAWCHD.KS.L.KMKSCLEFSLRIQEFIELIRQNKRLDAVRHARKHF.Q.EGS. | |
| Retrocopy | AKEVEESLERCETATCLAWCHD-KSWLWKMKSCLEFSLRIQEFIELIRQNKRLDAVRHARKHFTQVEGS* |
| Parental | LDEVRQAMGMLAFPPDTHISPYKPCLSQVKSALTLQR-VEIRAFTLQRVDIRVKSALTLQRVDIRVKSAL |
| LDEVRQAMGMLAF.PDTH.SPYK............Q..V......L..........LTLQ......K... | |
| Retrocopy | LDEVRQAMGMLAFLPDTHVSPYKDLRDPARWRILIQQ<VPV*QYRLHQLGNNSVFTLTLQAGLSAIKTP- |
| Parental | QCYKEDGSSKSPDC-PVCSRSLNKLAQPLP-MAHCANSRLVCKISGDVMNENNPPRMLPNGYVYGYNSLL |
| Q.YKEDGSSKSPDC.P...........P.P.MAHCANSRL..KISGDVMN.NN.P.MLPNGYVYGYNSLL | |
| Retrocopy | QYYKEDGSSKSPDC<PCAAAPSTSWRSPCP<MAHCANSRLDYKISGDVMNHNNLPMMLPNGYVYGYNSLL |
| Parental | SIRQDDKVVCPRTKEVFHFSQAEKVYIM |
| SIRQDDKV.CPRTKEVFHFS.AEKVYIM | |
| Retrocopy | SIRQDDKVICPRTKEVFHFS*AEKVYIM |
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 .31 RPM | 4 .90 RPM |
| SRP051959_heart | 0 .26 RPM | 6 .12 RPM |
| SRP051959_kidney | 0 .27 RPM | 5 .57 RPM |
| SRP051959_liver | 0 .32 RPM | 3 .36 RPM |
| SRP051959_lung | 0 .65 RPM | 7 .24 RPM |
| SRP051959_lymph_node | 0 .41 RPM | 6 .35 RPM |
| SRP051959_skeletal_muscle | 0 .24 RPM | 4 .06 RPM |
| SRP051959_spleen | 0 .44 RPM | 5 .80 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3821 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3821 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3821 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 | ENSCJAG00000001587 | 2 retrocopies |
retro_cjac_3821 , retro_cjac_567,
|