RetrogeneDB ID: retro_ptro_773

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 12:75148967..75149571(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNG2
• Ensembl ID: ENSPTRG00000016196
• Aliases: None
• Description: None

Sequence

>retro_ptro_773
ATCAAATATAAAAAATATTAAGATCTAAGAGGTTTAACTAACTTTTTTTGAATCTTCTCCAGAAACTTTTATTGTGGCTG
CCAATATTTTGGACAGATCCTTGGCTTTTCTGAAGGTGAAACCTAAAATTCATCTTTCACTGGGGTCTGTTGTTTATGCT
GGTTGCCAGAATAGTTGAAAAAGAATGCAATGTTTTATCTGCTCATGAAGTAATCTTGATCCGTCAATGTAAACGCACTG
CTTCTTCTGACAGAAAACTGATGGAAAAATAATTTCAGAAAAAAATTTGGAACTATGAATTGGAACGTACTGTACCTTAA
ACTTCTTTTGCTTCTATAAGACTCATATTTCTTTATATTTGAGAAAGGAAAGAAATATTGGGCCTTATAAACCGGAAGCT
CAGCTGAAAACTTGCAATTTTTTGCTAATGTTTTCAAAAGCAAAACCATCTGTATTAGTTTTGTGTCTTCTTAATCTGGA
AGTAGAACTGTTGTAATTTACTGAATTATTGAAAAATGTCCTGCTTCTTATAAGGCATTCAAAGATTAATGACACTGAAT
TCTTTTAGTGGAGGGAACTAGTTTCTAAATGCCTAGCTGAATAT

Alignment

ORF - retro_ptro_773 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.94 %
• Parental protein coverage: 58.43 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LRNAKVEDLRSLANFF-GSCTETFVLAVNILDRFLALMKVKPK-HLSCIGVCS-FLLAARIVEEDCNIPS
          ....K..DLR.L.NFF..S..ETF..A.NILDR.LA..KVKPK...S..GVC..F.L.ARIVE..CN..S
Retrocopy IKYKKY*DLRGLTNFF>ESSPETFIVAANILDRSLAFLKVKPK<NSSFTGVCC<FMLVARIVEKECNVLS

Parental  THDVIRISQCKCTA-SDIKRMEKIISEKL-HYELEATT-ALNFLHLYHTIILCHTSERKEILSLDKLEAQ
          .H.VI.I.QCK.TA.SD.K.MEK....K...YELE.T...LNF...Y.T.I.........I....K.EAQ
Retrocopy AHEVILIRQCKRTASSDRKLMEK*FQKKIWNYELERTV<TLNFFCFYKTHISLYLRKERNI-GPYKPEAQ

Parental  LKACNCRLIFSKAKPSVLALCLLNLEVETLKSVELLEILLLVKKHSKINDTEFFYWRELVSKCLAEY
          LK.CN..L.FSKAKPSVL.LCLLNLEVE.L...ELL...LL...HSKINDTEFF.WRELVSKCLAEY
Retrocopy LKTCNFLLMFSKAKPSVLVLCLLNLEVELL*FTELLKNVLLLIRHSKINDTEFF*WRELVSKCLAEY

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
SRP007412_brain_prefrontal_cortex	0.02 RPM	24.13 RPM
SRP007412_cerebellum	0.00 RPM	57.14 RPM
SRP007412_heart	0.00 RPM	4.55 RPM
SRP007412_kidney	0.00 RPM	48.90 RPM
SRP007412_liver	0.00 RPM	6.78 RPM
SRP007412_testis	0.11 RPM	6.85 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_773 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_773 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_773 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_879
Sus scrofa	retro_sscr_813

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013793	1 retrocopy	retro_amel_960,
Dasypus novemcinctus	ENSDNOG00000005210	1 retrocopy	retro_dnov_2498,
Felis catus	ENSFCAG00000026008	1 retrocopy	retro_fcat_1062,
Macropus eugenii	ENSMEUG00000008707	1 retrocopy	retro_meug_1962,
Macaca mulatta	ENSMMUG00000000914	1 retrocopy	retro_mmul_879,
Monodelphis domestica	ENSMODG00000011779	1 retrocopy	retro_mdom_358,
Nomascus leucogenys	ENSNLEG00000008169	1 retrocopy	retro_nleu_933,
Pongo abelii	ENSPPYG00000014867	1 retrocopy	retro_pabe_942,
Pan troglodytes	ENSPTRG00000016196	1 retrocopy	retro_ptro_773 ,
Sus scrofa	ENSSSCG00000008988	1 retrocopy	retro_sscr_813,
Ictidomys tridecemlineatus	ENSSTOG00000027922	1 retrocopy	retro_itri_1112,
Tupaia belangeri	ENSTBEG00000007671	2 retrocopies	retro_tbel_2258, retro_tbel_38,
Tursiops truncatus	ENSTTRG00000014837	1 retrocopy	retro_ttru_491,