RetrogeneDB ID: retro_cjac_1888

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:16338795..16339300(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HAX1
• Ensembl ID: ENSCJAG00000009660
• Aliases: None
• Description: HCLS1 associated protein X-1 [Source:HGNC Symbol;Acc:16915]

Sequence

>retro_cjac_1888
ACCCATCTTTCTGAACTTCCAGGTCCTGAGGCAGAGACACCTGGTGAGAGACTGCGGTAGGGACGAACACTTCGGGACTC
AGTGCTTAAGTATCCAGAGAGTCACCAGCCCAGGATCTTTGGGGGGCTCTTGGAGAGTGATGCAAGAAGTGAATCCCCCA
AACCAGCACCAGACTGGGGCTCCCATAGGTTTGATGACATATGGCCTGTGGACCCCATCCTAGAACCAGAGAGGACAATG
ATCTTTTTTCCCGGGTTGCCCAGGAGGGTCTTGGCTCGGTTCTACAGCCCCAGCCTCAATCCTATTTCAAGAGCATCTCT
GTGACCAAGATCACTAAGCCAGACGGGAGAGTGGAGGAGCGCAGGACAGCGGTGGACAGTGAGGGCTGGACAGAGGCCGC
AATAACTGGACATGAAGCAGATAGCAGTCCTAGGGTGATCCAGAATCACCAAGACCTCCAGCCCTGGATGATGCCTTCTC
CATCCTGGACTTATTCCTAGGACGT

Alignment

ORF - retro_cjac_1888 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.86 %
• Parental protein coverage: 62.91 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SHLPELPGPESETPGERLREGQTLRDSMLKYPDSHQPRIFGGVLESDARSESPKPTPYWGFQRPFHRFDD
          .HL.ELPGPE.ETPGERLR.G.TLRDS.LKYP.SHQPRIFGG.LESDARSESPKP.P.WG..R....FDD
Retrocopy THLSELPGPEAETPGERLR*GRTLRDSVLKYPESHQPRIFGGLLESDARSESPKPAPDWGSHR----FDD

Parental  IWPVD-PHPRTREDNDLDAQVAQEGLGSVLQPQPKSYFKSISVTKITKPDGVVEERRTVVDSEGRTETTV
          IWPVD.PHPRTREDNDL...VAQEGLGSVLQPQP.SYFKSISVTKITKPDG.VEERRT.VDSEG.TE...
Retrocopy IWPVD<PHPRTREDNDLFSRVAQEGLGSVLQPQPQSYFKSISVTKITKPDGRVEERRTAVDSEGWTEAAI

Parental  TRHEADSSPR-GDPESPRLPALDDAFSILDLFLGR
          T.HEADSSPR.GDPESPR.PALDDAFSILDLFLGR
Retrocopy TGHEADSSPR<GDPESPRPPALDDAFSILDLFLGR

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	11.23 RPM
SRP051959_heart	0.07 RPM	17.84 RPM
SRP051959_kidney	0.00 RPM	14.13 RPM
SRP051959_liver	0.00 RPM	18.56 RPM
SRP051959_lung	0.00 RPM	12.23 RPM
SRP051959_lymph_node	0.00 RPM	13.81 RPM
SRP051959_skeletal_muscle	0.00 RPM	34.22 RPM
SRP051959_spleen	0.02 RPM	13.78 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1888 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1888 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1888 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009660	1 retrocopy	retro_cjac_1888 ,
Dasypus novemcinctus	ENSDNOG00000016727	1 retrocopy	retro_dnov_1537,
Dipodomys ordii	ENSDORG00000012587	1 retrocopy	retro_dord_769,
Homo sapiens	ENSG00000143575	1 retrocopy	retro_hsap_4912,
Microcebus murinus	ENSMICG00000010414	2 retrocopies	retro_mmur_1118, retro_mmur_1284,
Monodelphis domestica	ENSMODG00000017215	1 retrocopy	retro_mdom_433,
Mus musculus	ENSMUSG00000027944	3 retrocopies	retro_mmus_1306, retro_mmus_2000, retro_mmus_353,
Nomascus leucogenys	ENSNLEG00000011290	1 retrocopy	retro_nleu_2286,
Pan troglodytes	ENSPTRG00000001380	1 retrocopy	retro_ptro_3275,
Rattus norvegicus	ENSRNOG00000045647	1 retrocopy	retro_rnor_736,
Tupaia belangeri	ENSTBEG00000014445	1 retrocopy	retro_tbel_930,