RetrogeneDB ID: retro_cjac_967

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 12:32599640..32600352(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HTATIP2
• Ensembl ID: ENSCJAG00000006718
• Aliases: None
• Description: None

Sequence

>retro_cjac_967
GCGAAGCTTCGGGAAGACTTCAGGATGCAGAATAAATCCGTCTTTTATTTGGGCGCCAGTGGAGAAACCACCGGCAGAGT
GCTCTTAAAGGAAATCTGGGGAGGGCTTGTTTTCCAAAGTCACTCTCATTGGCCGGAGGAAGCTCGCCTTCAACAAGGAA
GTTTATAAAAATGTGAATCAATGAGTGGTGGACGTTGAAAGATTGGATTACTACGCTTCTGCCTTTCAAGGTCATGATGT
TGGATTCTGTTGCCTGGGTACCACCAGAGGGAAAGCTGGGGCGGAGGGATTTGTTCGTGTTGAGCGAGATGATGTGCTGA
AGTCTGCAGAGCTGGCAAAAGCTGGACGGTGCAAACATTTCAACTCTGTATCATATTCTAAAGGAGCTGAAAAGTGAAGC
AGTTTTTTAATACTGCAAGTTAAGGGAGAAGTGGAAGCCAGATCTGAAGAATTAAAGTTTGATCCGTATTCTGTTTTTAG
GCCTGGAGTTCTGTTGCGTGATAGGCAAGAATCTTGCCCAGGTAATGTATGTTTGCTTAGAAAGTTCGTTGGCTCCTTAC
CAGATTCTTGGGCTACTGAGCATTCTGTGCCTGTGGTGACTGTGGTTAGAGCAATGCTGAACAATGCGGTGAGAACAAGT
GACAAGATGATGATCCTGCTGGAAAACAAGGCCATCCATGACGTGGGGAAAGCGCACGGCTCTCTCAAGCCG

Alignment

ORF - retro_cjac_967 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.83 %
• Parental protein coverage: 96.71 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SKLREDFRMQNKSVFILGASGE-TGRVLLKEI-LEQALF-SKVTLIGRRKLTFEEEAYKNVNQELVDFEK
          .KLREDFRMQNKSVF.LGASGE.TGRVLLKEI.L..A.F.SKVTLIGRRKL.F..E.YKNVNQ..VD.E.
Retrocopy AKLREDFRMQNKSVFYLGASGETTGRVLLKEI<LGRACF<SKVTLIGRRKLAFNKEVYKNVNQ*VVDVER

Parental  LDDYASAFQGHDVGFCCLGTTRVKAGAEGFVRVDRDYVLRSAELAKAGGCKHFNLLS-SKGADKSSSFLY
          LD.YASAFQGHDVGFCCLGTTR.KAGAEGFVRV.RD.VL.SAELAKAG.CKHFN..S.SKGA.K.SSFL.
Retrocopy LDYYASAFQGHDVGFCCLGTTRGKAGAEGFVRVERDDVLKSAELAKAGRCKHFNSVSYSKGAEK*SSFLI

Parental  LQVKGEVEARVEELKFDRYSVFRPGVLLCDRQESRPGE-WFVRKFFGSLPASWASGHSVPVVTVVRAMLN
          LQVKGEVEAR.EELKFD.YSVFRPGVLL.DRQES.PG.....RKF.GSLP.SWA..HSVPVVTVVRAMLN
Retrocopy LQVKGEVEARSEELKFDPYSVFRPGVLLRDRQESCPGNVCLLRKFVGSLPDSWATEHSVPVVTVVRAMLN

Parental  NAVRPSDKKMELLENKAIHDLGKADGSLKP
          NAVR.SDK.M.LLENKAIHD.GKA.GSLKP
Retrocopy NAVRTSDKMMILLENKAIHDVGKAHGSLKP

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	0.02 RPM	10.10 RPM
SRP051959_heart	0.02 RPM	6.42 RPM
SRP051959_kidney	0.00 RPM	13.38 RPM
SRP051959_liver	0.00 RPM	9.73 RPM
SRP051959_lung	0.00 RPM	13.06 RPM
SRP051959_lymph_node	0.00 RPM	8.31 RPM
SRP051959_skeletal_muscle	0.00 RPM	11.97 RPM
SRP051959_spleen	0.00 RPM	13.55 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_967 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_967 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_967 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006718	1 retrocopy	retro_cjac_967 ,
Loxodonta africana	ENSLAFG00000018703	1 retrocopy	retro_lafr_244,
Oryctolagus cuniculus	ENSOCUG00000000749	1 retrocopy	retro_ocun_822,
Pongo abelii	ENSPPYG00000003421	1 retrocopy	retro_pabe_1288,
Ictidomys tridecemlineatus	ENSSTOG00000011216	2 retrocopies	retro_itri_1354, retro_itri_1523,