RetrogeneDB ID: retro_pabe_1114

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 14:57604372..57605018(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZCCHC7
• Ensembl ID: ENSPPYG00000029763
• Aliases: None
• Description: zinc finger, CCHC domain containing 7 [Source:HGNC Symbol;Acc:26209]

Sequence

>retro_pabe_1114
CTAACGACCAAACCCGGACACTCAAAAAGCCAAAGACCCCTTCAAAACCATCAGCCTTAGTATATTGCTGTCACTGCATG
CAAAAGGCCATTATGGACACAAGTCCATAATGAAGAGAAGTGTACCACCTGTCTCCAGTATCTCCATTCATCTGCTACTA
TGATGACAAATATGAAGTTAAGGAGAGAGAAAAGAGAGTAAAACAAAAAATAAAAGTACTCAAGAGGAGTGGGGATATCC
CAGAGCCATCCAAGCTACCTTACATAAAAGCAGCAAATGAGAACCCCCATCATGATATAAAGAAGGGCTGTGCCTCATGG
AAAAGCAACAGGTGGCCTCAAGAAAACAAAGAAACACAAAAAGAAACGAAGAACAAGAATGAAAACTGAGAGAAGCACAG
GAAGGCTGACAGACATCGTGAAGTGGATGAGGATTTTCCCTGGGGCCCCAAAACCTACTCTTCTCCTGGCAGTTTAAAAA
CCCAGAAGCCTTCCAAGCCCTTTCATCATTCATCGCATTACCATATGTCGAGAGAAGACAAGTCTCCCAAGGAGGGTAAG
AAGGGCAAGAGAAGAAAAAGGAGAGATGCTTGGAAGATGATGACAATGATAACTTATTTCTTATTAAGGAGAGGGAAAAA
AAGTCT

Alignment

ORF - retro_pabe_1114 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.23 %
• Parental protein coverage: 99.54 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LQTKPGPPK-KPKTPSRPSALAYCYHCAQKGHYGHECPEREVYDPSPVSPFICYYDDKYEIQEREKRLKQ
          L.TKPG..K.KPKTPS.PSAL.YC.HC.QK.........REVY..SPVSPFICYYDDKYE..EREKR.KQ
Retrocopy LTTKPGHSK<KPKTPSKPSALVYCCHCMQKAIMDTSP**REVYHLSPVSPFICYYDDKYEVKEREKRVKQ

Parental  KIKVLKKNGVIPEPSKLPYIKAANENPHHDIRKGRTSWKSNRWPQENKETQKEMKNKNRNWEKHRKADRH
          KIKVLK..G.IPEPSKLPYIKAANENPHHDI.KG..SWKSNRWP.................EKHRKADRH
Retrocopy KIKVLKRSGDIPEPSKLPYIKAANENPHHDIKKGCASWKSNRWPXXXXXXXXXXXXXXXXXEKHRKADRH

Parental  REVDEDFPRGPKTYSSPGSFKTQKPSKPFHRSSHYHTSREDKSPKEGKRGK-QKKKERCLEDDDNDNLFL
          REVDEDFP.GPKTYSSPGS.KTQKPSKPFH.SSHYH.SREDKSPKEGK.GK..KKKERCLEDDDNDNLFL
Retrocopy REVDEDFPWGPKTYSSPGSLKTQKPSKPFHHSSHYHMSREDKSPKEGKKGK<EKKKERCLEDDDNDNLFL

Parental  IKQRKKKS
          IK.R.KKS
Retrocopy IKEREKKS

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	0.44 RPM	3.21 RPM
SRP007412_cerebellum	0.00 RPM	5.47 RPM
SRP007412_heart	0.12 RPM	1.84 RPM
SRP007412_kidney	0.20 RPM	4.11 RPM
SRP007412_liver	0.18 RPM	5.02 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1114 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1114 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1114 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000147905	1 retrocopy	retro_hsap_1342,
Macaca mulatta	ENSMMUG00000007421	1 retrocopy	retro_mmul_2180,
Pongo abelii	ENSPPYG00000029763	1 retrocopy	retro_pabe_1114 ,
Pan troglodytes	ENSPTRG00000020939	2 retrocopies	retro_ptro_2962, retro_ptro_917,
Tursiops truncatus	ENSTTRG00000006054	2 retrocopies	retro_ttru_1606, retro_ttru_505,