RetrogeneDB ID: retro_cjac_1461

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 16:29332557..29333547(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BAT1
• Ensembl ID: ENSCJAG00000003152
• Aliases: DDX39B, BAT1
• Description: None

Sequence

>retro_cjac_1461
AATGGGGAAGAATGCGATTTGGAAAACGAGCTTTTGGATTATGACAAAGAGGAAGAGCCCACGCCAGCTACCCATAAAAA
AGACGTCGAGGGATCCTACGTTTCCATCCCCAGTTCTGGCTTCTGGTACTTTCTGCTGAAGCCGGAACTCCTTTGGGCTA
TCGTGGACTGTGGCTTTGAGCATCCATCTGAGGTCCAGCACGAGTGCATTCCCCAGGCCATCCTGGGCATGAACGTCCTG
TGCCAGGCCAAGTCTCGGATGGGCAAGACAGCGGTATTCGTGCTGGCCACCCTGCAGCAGATCGAGCCCGTCAGCAGACA
GGTTATGGCCCTGGTCCTGTGCCACACGAGGGAGCTGGCCTTCCAGATCAGCAAGGAATACCAATGCTTCTCCAAGTACA
TATCCAGCGTCAAGTTGTCTATGTTCTTCGGGGGCCTCTCCATCAAGAAGGATGAAGAAGTGTTGAAGAAGAACTGTCCC
ATGTTGTGGTGGGGACCCCAGGCCACATCCTGGTGCCTGGGCTGAACAGGAGCTTCAGCCAAAAGAACGTGAAGCACTTT
GTGCTGGACGAGTGAGACAAGATGCTGGAGCAGCTAAACATGCGGTGGGACATGCAGGAGATCTTCTGCCTGACACCGCT
CGAGAAGCAGTGCAGGATGTTCAGCGCCACCCTGAGCAAGGACATCCGGCCTGTGTGCAGGAAGTTTATGCAGGATCCCA
TGGAAGTGTTTGTGGATGACAAGACCAATCTCACCCTGCACGGACTGCAGCAGTACTGCCTCAAACTCAAAGACACTGAG
AAGACCCTCAAGCTCTTTGAACTCCTCCTGGACATGCTGGAGTTTAACCAGGTGATAATCTTCATCAAGTCAGTGCAACG
CTGCATAACCCTGGCCCAGCTCCTTGTGGTGCAGAAAGAACTTCCTGGCCTTTGGAATCCACTGGGACATGGCCCATAAG
GGGCACCTGTCACATTATCAGCAGTTCAGG

Alignment

ORF - retro_cjac_1461 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.48 %
• Parental protein coverage: 76.64 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DNELLDYEDDEVETAAGGDGAEAPAKKDVKGSYVSIHSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECI
          ..E..D.E..............A..KKDV.GSYVSI.SSGF..FLLKPELL.AIVDCGFEHPSEVQHECI
Retrocopy NGEECDLENELLDYDKEEEPTPATHKKDVEGSYVSIPSSGFWYFLLKPELLWAIVDCGFEHPSEVQHECI

Parental  PQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVA
          PQAILGM.VLCQAKS.MGKTAVFVLATLQQ.EPV..QV..LV.CHTRELAFQISKEY..FSKY...VK..
Retrocopy PQAILGMNVLCQAKSRMGKTAVFVLATLQQIEPVSRQVMALVLCHTRELAFQISKEYQCFSKYISSVKLS

Parental  VFFGGLSIKKDEEVLKKNCP-HIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIF
          .FFGGLSIKKDEEVLKKNCP.H.VVGTPG.IL....N.S...K..KHF.LDE.DKMLEQL.MR.D.QEIF
Retrocopy MFFGGLSIKKDEEVLKKNCP<HVVVGTPGHILVPGLNRSFSQKNVKHFVLDE*DKMLEQLNMRWDMQEIF

Parental  RMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNEKNRKLFD-LLDV
          ..TP.EKQ..MFSATLSK.IRPVCRKFMQDPME.FVDD.T.LTLHGLQQY..KLKD.EK..KLF..LLD.
Retrocopy CLTPLEKQCRMFSATLSKDIRPVCRKFMQDPMEVFVDDKTNLTLHGLQQYCLKLKDTEKTLKLFELLLDM

Parental  LEFNQVVIFVKSVQRCIALAQLL-VEQNFPAI-AIHRGMPQEERLSRYQQFK
          LEFNQV.IF.KSVQRCI.LAQLL.V....P....IH..M.....LS.YQQF.
Retrocopy LEFNQVIIFIKSVQRCITLAQLLVVQKELPGL>GIHWDMAHKGHLSHYQQFR

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	0.11 RPM	43.18 RPM
SRP051959_heart	0.05 RPM	45.43 RPM
SRP051959_kidney	0.07 RPM	51.09 RPM
SRP051959_liver	0.13 RPM	35.59 RPM
SRP051959_lung	0.02 RPM	55.28 RPM
SRP051959_lymph_node	0.14 RPM	64.20 RPM
SRP051959_skeletal_muscle	0.04 RPM	57.28 RPM
SRP051959_spleen	0.19 RPM	56.05 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1461 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1461 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1461 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003152	1 retrocopy	retro_cjac_1461 ,
Macropus eugenii	ENSMEUG00000008264	2 retrocopies	retro_meug_1623, retro_meug_288,
Macaca mulatta	ENSMMUG00000008839	1 retrocopy	retro_mmul_1126,
Pongo abelii	ENSPPYG00000016433	1 retrocopy	retro_pabe_804,