RetrogeneDB ID: retro_cjac_310

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 13:41277631..41278633(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000023305
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SUGT1
• Ensembl ID: ENSCJAG00000003604
• Aliases: None
• Description: None

Sequence

>retro_cjac_310
ATGGCGGCGGCTGCAGCAGGACCTGCAACATCCCAGAGGTTTTTCCAGAGCTTCTCGGATGCTCTAATCGACGAGGACCC
CCAGGCGGCGTTAGAGGAGCTGACTAAGGCTTTAGAACAGAAACCAGATGATGCACAGTATTATTGTCAAAGAGCTTATT
GCCACATTCTTCTTGGGAATTACTGTGTTGCTGTTGCTGATGCAAAGAAGTCTCTCGAACTCAATCCAAATAATTCCACT
GCTATGTTGAGAAAAGGAATATGTGAATACCATGAAAAAAACTATGCTGCTGCTCTAGAAACTTTTATAGAAGGACAAAA
ATTAGATAGTGCAGATGCTAATTTCAGTGTCTGGATTAAAAGGTGTCAAGAAGCTCAGAATGACTCAGAATCTGAGGTGT
GGATTCATCAGTCAAAAATCAAGTATGACTGGTATCAAACAGAAGCTCAAGTAGTCATTACGCTTATGATCAAAAATGTT
CAGAAGAATGATGTAAATGTGGAATTTTCAGAAAAACAGTTGTCTGCTTTGGTTAAACTTCCTTCTGGAGAGGATTACAA
TTTGAAACTGGAACTTCTTCATCCTATAATACCAGAACAGAGCACATTTAAAGTATTTTCAACAAAGATTGAAATTAAAC
TGAAAAAGCCAGAGGCTGTGAGATGGGAAAAGCTAGAGGGGCAAGGAGATGTGCCTACGCCAAAACAATTCATAGCAGAT
GTAAAGAACCTATATCCATCATCATCTCCTTATACAAGAAATTGGGATAAATTGGTTGGTGAGATAAAAGAAGAAGAAAA
GAATGAAAAGTTGGAGGGAGATGCAGCCTTAAACAAATTATTTCAGCAGATCTATTCAGATGGTTCTGATGAAGTGAAAC
GTGCCATGAACAAATCCTTTATGGAGTCTGGTGGTACAGTTTTGAGTACCAACTGGTCTGATGTAGGTAAAAGGAAAGTT
GAAATCAATCCTCCTGATGATATGGAATGGAAAAAGTACTAA

Alignment

ORF - retro_cjac_310 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.8 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAAAAGPATSRRFFQSFSDALIDEDPQAALEELTKALEQKPDDAQYYCQRAYCHILLGNYCVAVADAKK
          MAAAAAGPATS.RFFQSFSDALIDEDPQAALEELTKALEQKPDDAQYYCQRAYCHILLGNYCVAVADAKK
Retrocopy MAAAAAGPATSQRFFQSFSDALIDEDPQAALEELTKALEQKPDDAQYYCQRAYCHILLGNYCVAVADAKK

Parental  SLELNPNNSTAMLRKGICEYHEKNYAAALETFIEGQKLDSADANFSVWIKRCQEAQNGSESEVWIHQSKI
          SLELNPNNSTAMLRKGICEYHEKNYAAALETFIEGQKLDSADANFSVWIKRCQEAQN.SESEVWIHQSKI
Retrocopy SLELNPNNSTAMLRKGICEYHEKNYAAALETFIEGQKLDSADANFSVWIKRCQEAQNDSESEVWIHQSKI

Parental  KYDWYQTESQVVITLMIKNVQKNDVNVEFSEKQLSALVKLPSGEDYNLKLELLHPIIPEQSTFKVLSTKI
          KYDWYQTE.QVVITLMIKNVQKNDVNVEFSEKQLSALVKLPSGEDYNLKLELLHPIIPEQSTFKV.STKI
Retrocopy KYDWYQTEAQVVITLMIKNVQKNDVNVEFSEKQLSALVKLPSGEDYNLKLELLHPIIPEQSTFKVFSTKI

Parental  EIKLKKPEAVRWEKLEGQGDVPTPKQFIADVKNLYPSSSPYTRNWDKLVGEIKEEEKNEKLEGDAALNKL
          EIKLKKPEAVRWEKLEGQGDVPTPKQFIADVKNLYPSSSPYTRNWDKLVGEIKEEEKNEKLEGDAALNKL
Retrocopy EIKLKKPEAVRWEKLEGQGDVPTPKQFIADVKNLYPSSSPYTRNWDKLVGEIKEEEKNEKLEGDAALNKL

Parental  FQQIYSDGSDEVKRAMNKSFMESGGTVLSTNWSDVGKRKVEINPPDDMEWKKY
          FQQIYSDGSDEVKRAMNKSFMESGGTVLSTNWSDVGKRKVEINPPDDMEWKKY
Retrocopy FQQIYSDGSDEVKRAMNKSFMESGGTVLSTNWSDVGKRKVEINPPDDMEWKKY

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	0.16 RPM	20.79 RPM
SRP051959_heart	0.12 RPM	21.00 RPM
SRP051959_kidney	0.16 RPM	21.65 RPM
SRP051959_liver	0.06 RPM	20.88 RPM
SRP051959_lung	0.16 RPM	24.71 RPM
SRP051959_lymph_node	0.25 RPM	27.03 RPM
SRP051959_skeletal_muscle	0.17 RPM	19.22 RPM
SRP051959_spleen	0.21 RPM	27.46 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_310 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_310 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_310 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008606	2 retrocopies	retro_amel_353, retro_amel_896,
Canis familiaris	ENSCAFG00000004823	1 retrocopy	retro_cfam_136,
Callithrix jacchus	ENSCJAG00000003604	1 retrocopy	retro_cjac_310 ,
Cavia porcellus	ENSCPOG00000003374	1 retrocopy	retro_cpor_110,
Dasypus novemcinctus	ENSDNOG00000002991	1 retrocopy	retro_dnov_2621,
Homo sapiens	ENSG00000165416	1 retrocopy	retro_hsap_2628,
Gorilla gorilla	ENSGGOG00000006797	1 retrocopy	retro_ggor_1840,
Nomascus leucogenys	ENSNLEG00000015700	1 retrocopy	retro_nleu_640,
Otolemur garnettii	ENSOGAG00000008220	1 retrocopy	retro_ogar_41,
Pan troglodytes	ENSPTRG00000005906	1 retrocopy	retro_ptro_1773,