RetrogeneDB ID: retro_pabe_2114

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b:46862453..46863080(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDK7
• Ensembl ID: ENSPPYG00000015525
• Aliases: None
• Description: cyclin-dependent kinase 7 [Source:HGNC Symbol;Acc:1778]

Sequence

>retro_pabe_2114
GTTGGAGGCTTTAAGTTTGCTGCGGTTTACAAGGCCAGAGATAAGAATACCAACCAAATTGTCGCCATTAAGAAAATCAA
ACTTGGACATAGATCAGAAGCTAAAGATGGTATAAATAGAACAGGCTTAGGAGAGATACAATTATTATAGGAGCTAAGTC
ATCCAAATATATTTGGTCTCCTTGATGCTTTTGGACGTAAGTCTAATATTAGCCTTATCTTTGGTTTTATGGAAACTGAT
CTAGAGGTTATAATAAAGGATAATAGTCTTGTGCTGACACCATCACACATCAAAGTCTGCATGTTGACCACTCTTCAAGG
ATTAGAATATTTACATCAACATTGGATCCTACATAGGGATCTGAAACCAAGCAACTTGTTGCTAGATGAAAATGGAGTTC
TAAAACTGGCAGATTTTGGCCTGGCCAAATCATGTGGGAGCGCCAATAGAGCTTATACACATCAGGTTGCAACCAGGTGG
TATCAGGCACCTGAGTTACTATTTGGAGCTAAGATGTATGGTGTAGGTGTGGACATGTGGCCTGTTGGCTGTATATTAGC
AGAGTTACTTCTAAGGGTTCCTTTTTTGTCAGGAGATTCAGACCTTGATCAGCTAACAAGAATATTT

Alignment

ORF - retro_pabe_2114 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.52 %
• Parental protein coverage: 60.4 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LGEGQFATVYKARDKNTNQIVAIKKIKLGHRSEAKDGINRTALREIKLLQELSHPNIIGLLDAFGHKSNI
          .G...FA.VYKARDKNTNQIVAIKKIKLGHRSEAKDGINRT.L.EI.LL.ELSHPNI.GLLDAFG.KSNI
Retrocopy VGGFKFAAVYKARDKNTNQIVAIKKIKLGHRSEAKDGINRTGLGEIQLL*ELSHPNIFGLLDAFGRKSNI

Parental  SLVFDFMETDLEVIIKDNSLVLTPSHIKAYMLMTLQGLEYLHQHWILHRDLKPNNLLLDENGVLKLADFG
          SL.F.FMETDLEVIIKDNSLVLTPSHIK..ML.TLQGLEYLHQHWILHRDLKP.NLLLDENGVLKLADFG
Retrocopy SLIFGFMETDLEVIIKDNSLVLTPSHIKVCMLTTLQGLEYLHQHWILHRDLKPSNLLLDENGVLKLADFG

Parental  LAKSFGSPNRAYTHQVVTRWYRAPELLFGARMYGVGVDMWAVGCILAELLLRVPFLPGDSDLDQLTRIF
          LAKS.GS.NRAYTHQV.TRWY.APELLFGA.MYGVGVDMW.VGCILAELLLRVPFL.GDSDLDQLTRIF
Retrocopy LAKSCGSANRAYTHQVATRWYQAPELLFGAKMYGVGVDMWPVGCILAELLLRVPFLSGDSDLDQLTRIF

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	5.25 RPM
SRP007412_cerebellum	0.00 RPM	7.05 RPM
SRP007412_heart	0.00 RPM	2.44 RPM
SRP007412_kidney	0.03 RPM	5.80 RPM
SRP007412_liver	0.00 RPM	3.30 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2114 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2114 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2114 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2335
Pan troglodytes	retro_ptro_1707
Gorilla gorilla	retro_ggor_1772

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000134058	1 retrocopy	retro_hsap_2335,
Gorilla gorilla	ENSGGOG00000013349	1 retrocopy	retro_ggor_1772,
Mus musculus	ENSMUSG00000069089	1 retrocopy	retro_mmus_383,
Otolemur garnettii	ENSOGAG00000010748	1 retrocopy	retro_ogar_986,
Procavia capensis	ENSPCAG00000002566	1 retrocopy	retro_pcap_318,
Pongo abelii	ENSPPYG00000015525	1 retrocopy	retro_pabe_2114 ,
Pan troglodytes	ENSPTRG00000016946	1 retrocopy	retro_ptro_1707,
Tupaia belangeri	ENSTBEG00000012193	2 retrocopies	retro_tbel_587, retro_tbel_637,