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 symbol: BECN1
• Ensembl ID: ENSCJAG00000013144
• Aliases: BECN1, beclin-1
• Description: beclin 1, autophagy related [Source:HGNC Symbol;Acc:1034]

Sequence

>retro_cjac_330
AAGGTGGGAGTCAGGCCCTCCGCCATGTCTTCCATCCGCTTCCTGTGCCAGCGCTGCAACCAGGCCCTGAAGCTGAGCTG
CTCCTCTGAGTCCGGGGTCTTCCCTGCAGCTTCGGCCCTCACCTCCGGGCAGGCTGAGCCCAGAGACACCCAGGAGCCCT
GCACCACCAGGGAGGTGACAGACGCTGAAGAGCCGCAGGACGGTGCCTCCAGCCCACCCCTTCCAGGGGATGGCTGTGTG
TCCAGCTACAGTGCCAGCATCTTCACCCTGCTGGGGAAGCTTGGCCCCATGCGGATGCTCAGCAGCATCCAGAAGGCAGC
TGGTGACATTTTTGACATCATCTCTGGCCAAGAAGATGTGGACCATCCCCTGTGTGAAGAGTGCACCGACAGTCTTCTAG
AGCAGTTGGACTTCCAGCTCGCTCTTACCGAAGGTGAGAGACAGAACTACCAACGCTGCCTGGAGAGCGGGGAGCTGGAG
ACCAGCGAGAAGGAGGTGGAGGCTCTGCGGGCGGAGCTGCGGGACCTGGAGCTGCAGGAGGCCAGGCTGGCCCAGGAGCT
GGAGGACGCGGATAGCAACCGTGCGAGAGCAGCCGCGGACCTCGAGGCAGCCCAGGCAGAGACTGCGGAGCTGGGCCAGC
AGGAGAGGCAGTGCTCCAGGGACTGCAGTGCCTTGGAGTACCAGCAGCTGGAACTGCTGGACCAGCTGGGGCACCTGGAG
AACCAGCTGCAGTATGCCAGGGTCCAGCTCGACCGGCTGGAGGAAATCAACTGCTTCAATGCCACATTTGAGGTCTGGGT
GGAGGGCCCCTTGGGCGTCATCAATAACTTCAGGTTGGGCTGCCTCCCCACTGTCCCTGTGAGCTGGAATGAGATTAATG
CTGCCTGGGGACAGGCGGCTTTGCTGCTCCTTGCCCTGGCCAATACAGTTGGTCTGGAGTTTCAGAGGTATCGACTCATG
CCCTGTGGAAACCATTCCTATCTCAAGTCTTTGACAGATGACCGCATGGAGCTGCCTTTGTTCTGTCATGGGGGGCAGGA
TGTTTTCTTCGATAATAAGTTTGACCGCGCCATGGTGGCCTTCCTGGACCTCATGCAGCAGTTCAAGGAAGAGGCTGAGA
AGGGTGAGTCCGGCCTCTGTCTGCCCTATGGGATCCAGGTGGAGAATGGCCTGATGGAAGACACTGGTGGCCTCAGGAAA
TGCTATTCCATCAGAACCCATCTGAACACGCAGGAGCTGTGGACAAAGGCCCTCAAGTTCATGCTCATAAACTTCAAGTG
GAGTCTCACCTGGGTTGCCTCAAGGTATCATCAAAAGTAG

Alignment

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

Expression

RNA-Seq

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

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_330 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_330 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_330 has 0 orthologous retrocopies within eutheria group .

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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	retro_fcat_62,
Macropus eugenii	ENSMEUG00000011700	1 retrocopy	retro_meug_600,
Monodelphis domestica	ENSMODG00000015064	1 retrocopy	retro_mdom_1778,