RetrogeneDB ID: retro_cjac_781

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:44599685..44600363(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000007137
• Aliases: None
• Description: None

Sequence

>retro_cjac_781
ATGGCCCAGAACTTGAAGGACTTGGCGGGACGCCTGCCCGCCGGGCCCCGGGGAATGGGCACCACGCTGAAGCTGCTGCT
GGGGACTGGCGCTGTGGCCTATGGTGTCCGCGAATCCGTGTTCACCGTGGAAGGCGGGCACAGAGCCATCTTCTTCAATC
GGATCGATGGAGTGCAGCGGGACACTATCCTGGCCGAGGGCCTTCACTTCAGAATCCCCTGGTTCCAGTACCCCATTATC
TATGACATTCGGGCCAGACCTCGGAAAATCTCCTCCCCCACAGGCTCCAAAGACCTGCAGATGGTGAATATCTCCCTGTG
AGGGCTGTCTCGACCCAATGCTCAGGAGCTTCCTAGCATGTACCAGCGCCTAGGGCTAGACTACAAGGAAGGAGTGTTGC
CGTCGATTGTCAAGGAGGTGCTCAAGAGTGTGGTGGCGAAGTTCAATGCCTCACAGCTGATCGCCCAGCACGCCCAGGTA
TCCCTGTTAATCTGCCGGGAGCTGACAGAGAGGGCCAAGGACTTCAGCCTCATACTGGATGATGTAGCCATCACAGAGGT
GAGCCTTAGCCGAGAGTACACAGCTGCTGTAGAAGCCAAACAAGTGGCCCAGCAGGAGGCCCAGCGGGCCCAGTTCTTGG
TAGAAGAAGCAAAGCAGGAACAGCGGCAGAAGATCGTG

Alignment

ORF - retro_cjac_781 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.36 %
• Parental protein coverage: 76.09 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAQNLKDLAGRLPAGPRGMGTALKLLLGAGAVAYGVRESVFTVEGGHRAIFFNRIGGVQQDTILAEGLHF
          MAQNLKDLAGRLPAGPRGMGT.LKLLLG.GAVAYGVRESVFTVEGGHRAIFFNRI.GVQ.DTILAEGLHF
Retrocopy MAQNLKDLAGRLPAGPRGMGTTLKLLLGTGAVAYGVRESVFTVEGGHRAIFFNRIDGVQRDTILAEGLHF

Parental  RIPWFQYPIIYDIRARPRKISSPTGSKDLQMVNISLRVLSRPNAQELPSMYQRLGLDYEERVLPSIVNEV
          RIPWFQYPIIYDIRARPRKISSPTGSKDLQMVNISL..LSRPNAQELPSMYQRLGLDY.E.VLPSIV.EV
Retrocopy RIPWFQYPIIYDIRARPRKISSPTGSKDLQMVNISL*GLSRPNAQELPSMYQRLGLDYKEGVLPSIVKEV

Parental  LKSVVAKFNASQLITQRAQVSLLIRRELTERAKDFSLILDDVAITELSFSREYTAAVEAKQVAQQEAQRA
          LKSVVAKFNASQLI.Q.AQVSLLI.RELTERAKDFSLILDDVAITE.S.SREYTAAVEAKQVAQQEAQRA
Retrocopy LKSVVAKFNASQLIAQHAQVSLLICRELTERAKDFSLILDDVAITEVSLSREYTAAVEAKQVAQQEAQRA

Parental  QFLVEKAKQEQRQKIV
          QFLVE.AKQEQRQKIV
Retrocopy QFLVEEAKQEQRQKIV

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	17.79 RPM
SRP051959_heart	0.05 RPM	16.59 RPM
SRP051959_kidney	0.00 RPM	24.23 RPM
SRP051959_liver	0.02 RPM	27.25 RPM
SRP051959_lung	0.00 RPM	12.46 RPM
SRP051959_lymph_node	0.05 RPM	14.68 RPM
SRP051959_skeletal_muscle	0.02 RPM	33.22 RPM
SRP051959_spleen	0.00 RPM	14.73 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_781 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_781 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_781 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013760	1 retrocopy	retro_amel_1928,
Canis familiaris	ENSCAFG00000014439	1 retrocopy	retro_cfam_1885,
Callithrix jacchus	ENSCJAG00000007137	1 retrocopy	retro_cjac_781 ,
Homo sapiens	ENSG00000215021	1 retrocopy	retro_hsap_624,
Gorilla gorilla	ENSGGOG00000004281	1 retrocopy	retro_ggor_547,
Macaca mulatta	ENSMMUG00000010205	2 retrocopies	retro_mmul_2599, retro_mmul_2623,
Nomascus leucogenys	ENSNLEG00000005021	2 retrocopies	retro_nleu_121, retro_nleu_450,
Pongo abelii	ENSPPYG00000004214	3 retrocopies	retro_pabe_419, retro_pabe_557, retro_pabe_559,
Rattus norvegicus	ENSRNOG00000012999	1 retrocopy	retro_rnor_2373,