RetrogeneDB ID: retro_cjac_2552

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:108121690..108122061(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BCAP31
• Ensembl ID: ENSCJAG00000011348
• Aliases: None
• Description: B-cell receptor-associated protein 31 [Source:HGNC Symbol;Acc:16695]

Sequence

>retro_cjac_2552
AACAAGCTCCTGTCTCCCTGTGGGAAACCTTCTAGCCACAGGCTGGGTCTGCAGTGGACTGCAGTTGCCACCTTCCTCTA
TGCGGAGGTCTTCGTTGTGTTCCTTCTCTGCATTCCCTTCATTTTTCACAAAAGATGGCAGATGATGTTCAAGTCCTGGC
TGGCAGAGTTGGTAGTGTCCTGTGGCAACACGTTCTTTGTGGTTTTCATTGTCATTCTTGTGCTGCTGGTCATCGACGCT
GCCCATGAGATTTGGAAGTATGATCATGTGACTGAGGAGGTGAACCTCAAATTCTGGGCCATGGAACACTCCACATGAAG
CTTTTCCATGCCCAGAGGAATCTCTACATTGCTGGCTTTTCCTTGCTGCTG

Alignment

ORF - retro_cjac_2552 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.53 %
• Parental protein coverage: 71.19 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NKLTSPCGKPSSNRMSLQWTAVATFLYAEVFVVLLLCIPFISPKRWQKIFKSRLVELVVSYGNTFFVVLI
          NKL.SPCGKPSS.R..LQWTAVATFLYAEVFVV.LLCIPFI..KRWQ..FKS.L.ELVVS.GNTFFVV.I
Retrocopy NKLLSPCGKPSSHRLGLQWTAVATFLYAEVFVVFLLCIPFIFHKRWQMMFKSWLAELVVSCGNTFFVVFI

Parental  VILVLLVIDAVREIRKYDDVTEKVNLQNNPGAMEH-FHMKLFRAQRNLYIAGFSLLL
          VILVLLVIDA..EI.KYD.VTE.VNL.....AMEH..HMKLF.AQRNLYIAGFSLLL
Retrocopy VILVLLVIDAAHEIWKYDHVTEEVNLKF--WAMEH<LHMKLFHAQRNLYIAGFSLLL

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	21.19 RPM
SRP051959_heart	0.02 RPM	15.08 RPM
SRP051959_kidney	0.00 RPM	27.51 RPM
SRP051959_liver	0.00 RPM	24.76 RPM
SRP051959_lung	0.00 RPM	16.97 RPM
SRP051959_lymph_node	0.00 RPM	14.20 RPM
SRP051959_skeletal_muscle	0.00 RPM	9.32 RPM
SRP051959_spleen	0.00 RPM	22.12 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2552 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2552 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2552 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019245	1 retrocopy	retro_cfam_482,
Callithrix jacchus	ENSCJAG00000011348	1 retrocopy	retro_cjac_2552 ,
Callithrix jacchus	ENSCJAG00000016329	1 retrocopy	retro_cjac_2669,
Echinops telfairi	ENSETEG00000008662	1 retrocopy	retro_etel_1522,
Macropus eugenii	ENSMEUG00000007345	3 retrocopies	retro_meug_1017, retro_meug_1867, retro_meug_208,
Monodelphis domestica	ENSMODG00000008300	2 retrocopies	retro_mdom_1110, retro_mdom_24,
Sarcophilus harrisii	ENSSHAG00000009111	1 retrocopy	retro_shar_31,