RetrogeneDB ID: | retro_cjac_330 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 19:38749745..38751065(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000021914 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | BECN1 | ||
| Ensembl ID: | ENSCJAG00000013144 | ||
| Aliases: | BECN1, beclin-1 | ||
| Description: | beclin 1, autophagy related [Source:HGNC Symbol;Acc:1034] |
Retrocopy-Parental alignment summary:
>retro_cjac_330
AAGGTGGGAGTCAGGCCCTCCGCCATGTCTTCCATCCGCTTCCTGTGCCAGCGCTGCAACCAGGCCCTGAAGCTGAGCTG
CTCCTCTGAGTCCGGGGTCTTCCCTGCAGCTTCGGCCCTCACCTCCGGGCAGGCTGAGCCCAGAGACACCCAGGAGCCCT
GCACCACCAGGGAGGTGACAGACGCTGAAGAGCCGCAGGACGGTGCCTCCAGCCCACCCCTTCCAGGGGATGGCTGTGTG
TCCAGCTACAGTGCCAGCATCTTCACCCTGCTGGGGAAGCTTGGCCCCATGCGGATGCTCAGCAGCATCCAGAAGGCAGC
TGGTGACATTTTTGACATCATCTCTGGCCAAGAAGATGTGGACCATCCCCTGTGTGAAGAGTGCACCGACAGTCTTCTAG
AGCAGTTGGACTTCCAGCTCGCTCTTACCGAAGGTGAGAGACAGAACTACCAACGCTGCCTGGAGAGCGGGGAGCTGGAG
ACCAGCGAGAAGGAGGTGGAGGCTCTGCGGGCGGAGCTGCGGGACCTGGAGCTGCAGGAGGCCAGGCTGGCCCAGGAGCT
GGAGGACGCGGATAGCAACCGTGCGAGAGCAGCCGCGGACCTCGAGGCAGCCCAGGCAGAGACTGCGGAGCTGGGCCAGC
AGGAGAGGCAGTGCTCCAGGGACTGCAGTGCCTTGGAGTACCAGCAGCTGGAACTGCTGGACCAGCTGGGGCACCTGGAG
AACCAGCTGCAGTATGCCAGGGTCCAGCTCGACCGGCTGGAGGAAATCAACTGCTTCAATGCCACATTTGAGGTCTGGGT
GGAGGGCCCCTTGGGCGTCATCAATAACTTCAGGTTGGGCTGCCTCCCCACTGTCCCTGTGAGCTGGAATGAGATTAATG
CTGCCTGGGGACAGGCGGCTTTGCTGCTCCTTGCCCTGGCCAATACAGTTGGTCTGGAGTTTCAGAGGTATCGACTCATG
CCCTGTGGAAACCATTCCTATCTCAAGTCTTTGACAGATGACCGCATGGAGCTGCCTTTGTTCTGTCATGGGGGGCAGGA
TGTTTTCTTCGATAATAAGTTTGACCGCGCCATGGTGGCCTTCCTGGACCTCATGCAGCAGTTCAAGGAAGAGGCTGAGA
AGGGTGAGTCCGGCCTCTGTCTGCCCTATGGGATCCAGGTGGAGAATGGCCTGATGGAAGACACTGGTGGCCTCAGGAAA
TGCTATTCCATCAGAACCCATCTGAACACGCAGGAGCTGTGGACAAAGGCCCTCAAGTTCATGCTCATAAACTTCAAGTG
GAGTCTCACCTGGGTTGCCTCAAGGTATCATCAAAAGTAG
ORF - retro_cjac_330 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 59.78 % |
| Parental protein coverage: | 99.72 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MSTESANSFTLIGEASDGGTMENLSRRLKVTGDLFDIMSGQTDVDHPLCEECTDTLLDQLDTQLNVTENE |
| .S..SA..FTL.G.....G.M..LS...K..GD.FDI.SGQ.DVDHPLCEECTD.LL.QLD.QL..TE.E | |
| Retrocopy | VSSYSASIFTLLGKL---GPMRMLSSIQKAAGDIFDIISGQEDVDHPLCEECTDSLLEQLDFQLALTEGE |
| Parental | CQNYKRCLEILE-QMNEDDSEQLQMELKELALEEERLIQELEDVEKNRQMVAENLEKVQAEAERLDQEEA |
| .QNY.RCLE..E....E...E.L..EL..L.L.E.RL.QELED...NR...A..LE..QAE...L.Q.E. | |
| Retrocopy | RQNYQRCLESGELETSEKEVEALRAELRDLELQEARLAQELEDADSNRARAAADLEAAQAETAELGQQER |
| Parental | QYQREYSEFKRQQLELDDELKSVENQMRYAQLQLDKLKKTNVFNATFHIWHSGQFGTINNFRLGRLPSVP |
| Q..R..S....QQLEL.D.L...ENQ..YA..QLD.L...N.FNATF..W..G..G.INNFRLG.LP.VP | |
| Retrocopy | QCSRDCSALEYQQLELLDQLGHLENQLQYARVQLDRLEEINCFNATFEVWVEGPLGVINNFRLGCLPTVP |
| Parental | VEWNEINAAWGQTVLLLHALANKMGLKFQRYRLVPYGNHSYLESLTDKSKELPLYCSGGLRFFWDNKFDH |
| V.WNEINAAWGQ..LLL.ALAN..GL.FQRYRL.P.GNHSYL.SLTD...ELPL.C.GG...F.DNKFD. | |
| Retrocopy | VSWNEINAAWGQAALLLLALANTVGLEFQRYRLMPCGNHSYLKSLTDDRMELPLFCHGGQDVFFDNKFDR |
| Parental | AMVAFLDCVQQFKEEVEKGETRFCLPYRMDVEKGKIEDTGGSGGSYSIKTQFNSEEQWTKALKFMLTNLK |
| AMVAFLD..QQFKEE.EKGE...CLPY...VE.G..EDTGG....YSI.T..N..E.WTKALKFML.N.K | |
| Retrocopy | AMVAFLDLMQQFKEEAEKGESGLCLPYGIQVENGLMEDTGGLRKCYSIRTHLNTQELWTKALKFMLINFK |
| Parental | WGLAWVSSQFYNK |
| W.L.WV.S....K | |
| Retrocopy | WSLTWVASRYHQK |
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 | 18 .46 RPM |
| SRP051959_heart | 0 .00 RPM | 19 .59 RPM |
| SRP051959_kidney | 0 .00 RPM | 25 .45 RPM |
| SRP051959_liver | 0 .00 RPM | 17 .59 RPM |
| SRP051959_lung | 0 .00 RPM | 22 .66 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 23 .24 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 29 .74 RPM |
| SRP051959_spleen | 0 .00 RPM | 22 .88 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_330 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_330 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_330 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000013144 | 1 retrocopy |
retro_cjac_330 ,
|
| Felis catus | ENSFCAG00000013136 | 1 retrocopy | |
| Macropus eugenii | ENSMEUG00000011700 | 1 retrocopy | |
| Monodelphis domestica | ENSMODG00000015064 | 1 retrocopy |