RetrogeneDB ID: retro_cjac_383

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:11686724..11687319(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: AMMECR1L
• Ensembl ID: ENSCJAG00000010743
• Aliases: None
• Description: None

Sequence

>retro_cjac_383
TTTAAAATGCTCTATTGTCACCTCTGTGTCCTCCTACAGCCACGACTTCCTAGATTCTCCAATGACCCCTTTCTGTGTCT
TGTGACATGGAAGGCAGAGAGGGAAAAGTGGCTTCTTGGCTGCATTGGGACGTTCTCGGCCATGAATCTTCATTCAGGAC
TCAGGGAATACATGTTAGCCATTGCACTTAAGGACAGCTGATTTCCCCTCCAATCTGAGAGGAGCTGCCTGAGCTTTTTC
GTTCTGTCTCTCTCCATACTAACTTTGAGGACGCTAGTGATTACCTGGACTGGGAGACAGGGGTCCATGGGATTCAAACT
GAATTCACTAATGAAAAAGGCATCAAATGTACAGCCTCGTTTTCACCTGAGGTTGCTAAGGAACAAGACTGGGATGAGAT
CCAGGCAATAGAGTCCTTGCCCTGGAAAGGTAACTTTAAGGCTCCAATTACCAGTGAATTCAGAAAAATGATCAAACTCA
CCAGGTACCAAAGTGAGAAGGTGACAATCAGTTTTGCAGAGTGTATCACTTCTTGACAACACTGTTTCCAGAACCATACT
CCTCTTCATGCCCTACTCCCTACAAGCATTACTCC

Alignment

ORF - retro_cjac_383 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.13 %
• Parental protein coverage: 63.87 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FDVLYCHLYGFPQPRLPRFTNDPYPLFVTWKTGRDKRLRGCIGTFSAMNLHSGLREYTLTSALKDSRFP-
          F..LYCHL....QPRLPRF.NDP....VTWK..R.K.L.GCIGTFSAMNLHSGLREY.L..ALKDS.FP.
Retrocopy FKMLYCHLCVLLQPRLPRFSNDPFLCLVTWKAEREKWLLGCIGTFSAMNLHSGLREYMLAIALKDS*FP<

Parental  PLTREELPKLFCSVSLLTNFEDASDYLDWEVGVHGIRIEFINEKGVKRTATYLPEVAKEQDWDQIQTIDS
          P...EELP.LF.SVSL.TNFEDASDYLDWE.GVHGI..EF.NEKG.K.TA...PEVAKEQDWD.IQ.I.S
Retrocopy PPI*EELPELFRSVSLHTNFEDASDYLDWETGVHGIQTEFTNEKGIKCTASFSPEVAKEQDWDEIQAIES

Parental  LLRKGGFKAPITSEFRKTIKLTRYRSEKVTISYAEYIASRQHCFQNGT-LHA-PPLYNHYS
          L..KG.FKAPITSEFRK.IKLTRY.SEKVTIS.AE.I.S.QHCFQN.T.LHA.P..Y.HYS
Retrocopy LPWKGNFKAPITSEFRKMIKLTRYQSEKVTISFAECITS*QHCFQNHTPLHA<PTPYKHYS

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	0.13 RPM	22.83 RPM
SRP051959_heart	0.16 RPM	14.98 RPM
SRP051959_kidney	0.24 RPM	25.85 RPM
SRP051959_liver	0.04 RPM	15.64 RPM
SRP051959_lung	0.11 RPM	25.54 RPM
SRP051959_lymph_node	0.02 RPM	26.60 RPM
SRP051959_skeletal_muscle	1.83 RPM	14.74 RPM
SRP051959_spleen	0.00 RPM	25.17 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_383 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_383 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_383 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009373	1 retrocopy	retro_chof_1566,
Callithrix jacchus	ENSCJAG00000010743	1 retrocopy	retro_cjac_383 ,
Equus caballus	ENSECAG00000023095	1 retrocopy	retro_ecab_1085,
Echinops telfairi	ENSETEG00000000510	1 retrocopy	retro_etel_9,
Homo sapiens	ENSG00000144233	1 retrocopy	retro_hsap_1227,
Gorilla gorilla	ENSGGOG00000014448	1 retrocopy	retro_ggor_961,
Myotis lucifugus	ENSMLUG00000006871	1 retrocopy	retro_mluc_684,
Macaca mulatta	ENSMMUG00000001987	1 retrocopy	retro_mmul_1302,
Mus musculus	ENSMUSG00000041915	2 retrocopies	retro_mmus_1330, retro_mmus_352,
Nomascus leucogenys	ENSNLEG00000015793	1 retrocopy	retro_nleu_700,
Pan troglodytes	ENSPTRG00000012437	1 retrocopy	retro_ptro_843,
Sarcophilus harrisii	ENSSHAG00000014762	1 retrocopy	retro_shar_86,