RetrogeneDB ID: retro_cjac_272

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:54742098..54742833(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000023309
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000021032
• Aliases: None
• Description: None

Sequence

>retro_cjac_272
TGTTGCACAGACTCTGGAACCATGAACATATTTGATCGAAAGATCAACTTTGATGTGCTTTTAAAATTTTCTCATATAAC
CCCCTCAACACAGCAGCACCTGAAGAAGGTCTACGCAAGTTTTGCCCTTTATATGTTTGTGGCGGCTGCGGGGGCCTATG
TCCATGTGATCACTCATTTCATTCAGGCTGGCCTGCTGTCTGCTTTGGGCTCCCTGATATTGATGATTTGGCTGATGGCA
ACACCTCACAGCCATGAAACTGAGCAAAAAAGACTGGGACTTCTTGCTGGATTTGCTTTCCTTACAGGAGTTGTCCTGGG
CCCTGCCCTGGAGTTTTGCATTGCCATCAACCCCAGCATCCTTCCCACCGCTTTCATGGGCACAGCAATGATCTTCACCT
GCTTTACCCTGAGTGCACTCTATGCCAAGCGTCGTAGCTACCTCTTTCTGGGAGGTATCTTGATGTCAGCCCTGAGCCTA
TTGCTTTTGTCTTCCCTGGGGAATGTTTTCTTTGGATCCATTTGGCTTTTCCAAGCAAACCTATATGTGGGACTGGTGGT
CATGTGTGGCTTTGTCCTTTTTGATACTCAACTCATTATTGAAAAGGCTGAAAATGGAGATCAAGATTATATCTGGCACT
GCATTGATCTCTTCTTAGATTTCATTACTCTCTTCAGAAAACTCACGATGATCCTGGCCATGAACGAAAAGGATAAGAAG
AAAGAGAAGAAATGA

Alignment

ORF - retro_cjac_272 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.89 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNIFDRKINFDALLKFSHITPSTQQHLKKVYASFALCMFVAAAGAYVHVITHFIQAGLLSALGSLILMIW
          MNIFDRKINFD.LLKFSHITPSTQQHLKKVYASFAL.MFVAAAGAYVHVITHFIQAGLLSALGSLILMIW
Retrocopy MNIFDRKINFDVLLKFSHITPSTQQHLKKVYASFALYMFVAAAGAYVHVITHFIQAGLLSALGSLILMIW

Parental  LMATPHSHETEQKRLGLLAGFAFLTGVGLGPALEFCIAINPSILPTAFMGTAMIFTCFTLSALYAKRRSY
          LMATPHSHETEQKRLGLLAGFAFLTGV.LGPALEFCIAINPSILPTAFMGTAMIFTCFTLSALYAKRRSY
Retrocopy LMATPHSHETEQKRLGLLAGFAFLTGVVLGPALEFCIAINPSILPTAFMGTAMIFTCFTLSALYAKRRSY

Parental  LFLGGILMSALSLLLLSSLGNVFFGSIWLFQANLYVGLVVMCGFVLFDTQLIIEKAENGDQDYIWHCIDL
          LFLGGILMSALSLLLLSSLGNVFFGSIWLFQANLYVGLVVMCGFVLFDTQLIIEKAENGDQDYIWHCIDL
Retrocopy LFLGGILMSALSLLLLSSLGNVFFGSIWLFQANLYVGLVVMCGFVLFDTQLIIEKAENGDQDYIWHCIDL

Parental  FLDFITLFRKLMMILALNEKDKKKEKK
          FLDFITLFRKL.MILA.NEKDKKKEKK
Retrocopy FLDFITLFRKLTMILAMNEKDKKKEKK

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	2.04 RPM	123.81 RPM
SRP051959_heart	0.54 RPM	46.69 RPM
SRP051959_kidney	5.59 RPM	328.24 RPM
SRP051959_liver	7.95 RPM	432.02 RPM
SRP051959_lung	2.16 RPM	103.31 RPM
SRP051959_lymph_node	1.58 RPM	71.46 RPM
SRP051959_skeletal_muscle	1.16 RPM	61.98 RPM
SRP051959_spleen	0.86 RPM	92.00 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_272 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_272 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_272 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018588	1 retrocopy	retro_btau_762,
Canis familiaris	ENSCAFG00000008400	2 retrocopies	retro_cfam_1220, retro_cfam_876,
Callithrix jacchus	ENSCJAG00000021032	1 retrocopy	retro_cjac_272 ,
Dasypus novemcinctus	ENSDNOG00000007882	2 retrocopies	retro_dnov_164, retro_dnov_857,
Macropus eugenii	ENSMEUG00000015590	4 retrocopies	retro_meug_1076, retro_meug_1706, retro_meug_2157, retro_meug_48,
Monodelphis domestica	ENSMODG00000004277	2 retrocopies	retro_mdom_210, retro_mdom_250,
Otolemur garnettii	ENSOGAG00000005137	2 retrocopies	retro_ogar_1074, retro_ogar_3470,
Pteropus vampyrus	ENSPVAG00000016821	1 retrocopy	retro_pvam_755,
Sarcophilus harrisii	ENSSHAG00000010366	1 retrocopy	retro_shar_622,
Ictidomys tridecemlineatus	ENSSTOG00000001165	2 retrocopies	retro_itri_1273, retro_itri_564,
Tarsius syrichta	ENSTSYG00000002427	1 retrocopy	retro_tsyr_916,