RetrogeneDB ID: retro_pabe_3074

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:77203647..77204336(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNB2
• Ensembl ID: ENSPPYG00000006517
• Aliases: None
• Description: cyclin B2 [Source:HGNC Symbol;Acc:1580]

Sequence

>retro_pabe_3074
GTTAATTCTAAACCTAAGAGTCATGTGACTATTAGGCATACCATTTTAGAATAAATTGGAAATAGAGTTACAGCCAGAGC
AGCACAAGTAGCTAAGAAAGCTCAGAACACCAAAGTACCAGTTCAACCCACGGAAACAATAAATGTCAACAAACAACTGA
AACCTACTGCTTCTGTGAAATAGTACAGATGGAAATGTTGGCTCCCAAGGGTCCTTCTCCCATACCTGAGGATGCCTCCA
TGAAAGAAGAGAACATCTGCCAAGCTTTTTCTGATGCCTTGCTCTACAAAATTGAGGATATTGATAACAAAGATTGGAAT
AACCCTCAGCTCTGCAGTGACTATGTTATCTATCAGTACCTCAGGCAGCTGGAGATTTTGCAGTTCATAAACCCACATGT
CTTAGATGGATGAGATATAAATGGACATAAGCATACCATCCTGGTAGACTGGTTGGTGCAAATCCACTCCAAGTTTAGGC
TTCTTCAGGAGACTCTGTATGTATGTGTTGCCATTATGGATTGATTTTTACTGGTTCAGCCAGTTTCCCAGAGGAAGCTT
CAACTAGTTTGGATTACTGCTCTGCTCTTGGCTTCTAAGTATGAGGAGATGTTTTCTCCAAATATTGAAGGCTTTATTTA
CATCACAGACAATGCTTATACTAGTTCCCAAATACAAGAAATGGAAACT

Alignment

ORF - retro_pabe_3074 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.55 %
• Parental protein coverage: 58.29 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VNSKVKSHVTIRRTVLEEIGNRVTTRAAQVAKKAQNTKVPVQPTKTTNVNKQLKPTASVK-PVQMEMLAP
          VNSK.KSHVTIR.T.LE.IGNRVT.RAAQVAKKAQNTKVPVQPT.T.NVNKQLKPTASVK..VQMEMLAP
Retrocopy VNSKPKSHVTIRHTILE*IGNRVTARAAQVAKKAQNTKVPVQPTETINVNKQLKPTASVK<IVQMEMLAP

Parental  KGPSPTPEDISMKEENLCQAFSDALLCKIEDIDNEDWENPQLCSDYVKDIYQYLRQLEVLQSINPHFLDG
          KGPSP.PED.SMKEEN.CQAFSDALL.KIEDIDN.DW.NPQLCSDYV..IYQYLRQLE.LQ.INPH.LDG
Retrocopy KGPSPIPEDASMKEENICQAFSDALLYKIEDIDNKDWNNPQLCSDYV--IYQYLRQLEILQFINPHVLDG

Parental  RDINGRMRAILVDWLVQVHSKFRLLQETLYMCIAIMDRFLQVQPVSRKKLQLVGITALLLASKYEEMFSP
          .DING....ILVDWLVQ.HSKFRLLQETLY.C.AIMD.FL.VQPVS..KLQLV.ITALLLASKYEEMFSP
Retrocopy *DINGHKHTILVDWLVQIHSKFRLLQETLYVCVAIMD*FLLVQPVSQRKLQLVWITALLLASKYEEMFSP

Parental  NIEDFVYITDNAYTSSQIREMET
          NIE.F.YITDNAYTSSQI.EMET
Retrocopy NIEGFIYITDNAYTSSQIQEMET

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	0.00 RPM	0.44 RPM
SRP007412_cerebellum	0.24 RPM	0.12 RPM
SRP007412_heart	0.00 RPM	0.30 RPM
SRP007412_kidney	0.00 RPM	0.70 RPM
SRP007412_liver	0.00 RPM	0.49 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3074 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3074 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3074 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3816
Pan troglodytes	retro_ptro_2597

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005269	1 retrocopy	retro_btau_1584,
Homo sapiens	ENSG00000157456	1 retrocopy	retro_hsap_3816,
Nomascus leucogenys	ENSNLEG00000011543	1 retrocopy	retro_nleu_212,
Otolemur garnettii	ENSOGAG00000012885	2 retrocopies	retro_ogar_1770, retro_ogar_2766,
Pongo abelii	ENSPPYG00000006517	2 retrocopies	retro_pabe_3073, retro_pabe_3074 ,
Pan troglodytes	ENSPTRG00000007123	1 retrocopy	retro_ptro_2597,
Ictidomys tridecemlineatus	ENSSTOG00000001275	1 retrocopy	retro_itri_229,
Tarsius syrichta	ENSTSYG00000013818	1 retrocopy	retro_tsyr_1402,