RetrogeneDB ID: retro_pabe_942

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 12:75701010..75701595(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNG2
• Ensembl ID: ENSPPYG00000014867
• Aliases: None
• Description: cyclin G2 [Source:HGNC Symbol;Acc:1593]

Sequence

>retro_pabe_942
GATCTAAGAGGTTTAACTAACTTTTTTTGAATCTTCTCCAGAAACTTTTATTGTGGCTGCCAATATTTTGGACAGATCCT
TGGTTTTTCTGAAGGTGAAACCTAAAATTTATCTTTCACTGGGGTCTGTTGTTTATGCTGGTTGCCAGAATAGTTGAAAA
AGAATGCAATGTTTTATCTACTCATAAAGTAATCTTGATTCGTCAATGTAAACCCACTGCTGCTTCTGACAGAAAACTGA
TGGAAAAATAATTTCAGAAAAAAATTCGGAACTATGAATTGGAACGTACCGTACCTCAAACTTCTTTTGCTTCTATAAGA
CTATCATATTTCTTTATATTTGAGAAAGGAAAGAAATATTGGGCCTTACAAACTGGAAGCTCAGCTGAAAACTTGCAATT
TTTTGCTAATGTTTTCAAAAGCAAAACCATCTGTATTAGTTTTGTGCCTTCTTAATCTGGAAGTAGAACCATTGTAATTT
ACTGAATTATTAAAAAATTTCCTGCTTCTTATAAGGCATTCAAAGATTAATGACACCGAATTCTTCTAGTGGAGGGAAGT
AGTTTCTAAATGCCTAGCTGAATAT

Alignment

ORF - retro_pabe_942 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.68 %
• Parental protein coverage: 56.4 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  DLRSLANFF-GSCTETFVLAVNILDRFLALMKVKPK-HLSCIGVCS-FLLAARIVEEDCNIPSTHDVIRI
          DLR.L.NFF..S..ETF..A.NILDR.L...KVKPK..LS..GVC..F.L.ARIVE..CN..STH.VI.I
Retrocopy DLRGLTNFF>ESSPETFIVAANILDRSLVFLKVKPK<NLSFTGVCC<FMLVARIVEKECNVLSTHKVILI

Parental  SQCKCTA-SDIKRMEKIISEKL-HYELEATT-ALNFLHLYHTIILCHTSERKEILSLD-KLEAQLKACNC
          .QCK.TA.SD.K.MEK....K...YELE.T....NF...Y.TII.....ERKEIL.L..KLEAQLK.CN.
Retrocopy RQCKPTAASDRKLMEK*FQKKIRNYELERTV<TSNFFCFYKTIIFLYI*ERKEILGLT<KLEAQLKTCNF

Parental  RLVFSKAKPSVLALCLLNLEVETLKSVELLEILLLVKKHSKINDTEFFYWRELVSKCLAEY
          .L.FSKAKPSVL.LCLLNLEVE.L...ELL...LL...HSKINDTEFF.WRE.VSKCLAEY
Retrocopy LLMFSKAKPSVLVLCLLNLEVEPL*FTELLKNFLLLIRHSKINDTEFF*WREVVSKCLAEY

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	0.06 RPM	18.69 RPM
SRP007412_cerebellum	0.00 RPM	13.38 RPM
SRP007412_heart	0.00 RPM	2.89 RPM
SRP007412_kidney	0.00 RPM	29.80 RPM
SRP007412_liver	0.00 RPM	8.17 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_942 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_942 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_942 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 15 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 ,
Pongo abelii	ENSPPYG00000016016	1 retrocopy	retro_pabe_3373,
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,