RetrogeneDB ID: retro_pabe_3373

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 8:153183704..153184253(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNG1
• Ensembl ID: ENSPPYG00000016016
• Aliases: CCNG1, CCNG
• Description: cyclin-G1 [Source:RefSeq peptide;Acc:NP_001126412]

Sequence

>retro_pabe_3373
AAGAGGAATGTCCCATTGGCAACTGACTTGATCCGAATAAGTCAATATAGGTTTACAGTTTGAGACTTGTTGAGAATGGA
AAAGATTGTATTGGAGGTGTGTTGGAAAGTCAAAGCTACTACTGCCTTTCAATTTCTGCAACTGTATTATTCACTCCTTC
AAGAGAACTTGCCACTTGAAAGGAGAAATAGCATTAATTTTGAAAGACTAGAAGCTCAACTTAAGATATGTCATTGCAGG
ATCATATTTTCTAAAGCAAAGCCTTCTGTGTTGGCATTGTCTATCATTGCATTAGAGATCCAAGCACAGAAGTGTGTAGA
GTTAACAGAAGGAATAGAATGTCTTCAGAAACATTCCAAGATAAATGGCAGAGATTAGATCTTCTGGCAAGAGCTTGTAT
CCAAGTGTTTAACTGAATATTCATCAAATAAGTGTTCCAAACCAAACGTTCAGAAGTTGAAATGGATTGTTTCTGGGCGT
ACTGCACGGCAATTGAAGCATAGCTACTACAGAATAACTCACCTTCCAACAATTCCTGAAATGGTCCCT

Alignment

ORF - retro_pabe_3373 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.11 %
• Parental protein coverage: 62.37 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ERNVPLATDLIRISQYRFTVSDLMRMEKIVLEKVCWKVKATTAFQFLQLYYSLLQENLPLERRNNINFER
          .RNVPLATDLIRISQYRFTV.DL.RMEKIVLE.VCWKVKATTAFQFLQLYYSLLQENLPLERRN.INFER
Retrocopy KRNVPLATDLIRISQYRFTV*DLLRMEKIVLE-VCWKVKATTAFQFLQLYYSLLQENLPLERRNSINFER

Parental  LEAQLKACHCRIIFSKAKPSVLALSIIALEIQAQKCVELTEGIECLQKLSKINGRDLTFWQELVSKCLTE
          LEAQLK.CHCRIIFSKAKPSVLALSIIALEIQAQKCVELTEGIECLQK.SKINGRD..FWQELVSKCLTE
Retrocopy LEAQLKICHCRIIFSKAKPSVLALSIIALEIQAQKCVELTEGIECLQKHSKINGRD*IFWQELVSKCLTE

Parental  YSSNKCSKPNVQKLKWIVSGRTARQLKHSYYRITHLPTIPEMVP
          YSSNKCSKPNVQKLKWIVSGRTARQLKHSYYRITHLPTIPEMVP
Retrocopy YSSNKCSKPNVQKLKWIVSGRTARQLKHSYYRITHLPTIPEMVP

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	0.22 RPM	13.82 RPM
SRP007412_cerebellum	1.34 RPM	20.55 RPM
SRP007412_heart	0.36 RPM	47.26 RPM
SRP007412_kidney	0.23 RPM	96.56 RPM
SRP007412_liver	0.18 RPM	44.80 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3373 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3373 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3373 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015341	1 retrocopy	retro_cjac_2319,
Cavia porcellus	ENSCPOG00000000880	1 retrocopy	retro_cpor_771,
Dasypus novemcinctus	ENSDNOG00000015166	1 retrocopy	retro_dnov_1275,
Monodelphis domestica	ENSMODG00000007651	1 retrocopy	retro_mdom_1018,
Mus musculus	ENSMUSG00000020326	1 retrocopy	retro_mmus_1534,
Oryctolagus cuniculus	ENSOCUG00000002129	3 retrocopies	retro_ocun_1287, retro_ocun_512, retro_ocun_615,
Pongo abelii	ENSPPYG00000014867	1 retrocopy	retro_pabe_942,
Pongo abelii	ENSPPYG00000016016	1 retrocopy	retro_pabe_3373 ,
Sarcophilus harrisii	ENSSHAG00000007465	2 retrocopies	retro_shar_328, retro_shar_490,