RetrogeneDB ID: retro_ptro_1707

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2B:161450832..161451459(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDK7
• Ensembl ID: ENSPTRG00000016946
• Aliases: None
• Description: None

Sequence

>retro_ptro_1707
GTTGGAGGCTTTAAGTTTGCCGTGGTTTACAAGGCCAGAGATAAGAATACCAACCAAATTGTCGCCATTAAGAAAATCAA
ACTTGGACATAGATCAGAAGCTAAAGATGGTATAAACAGAACAGCCTTAAGAGAGATACAATTATTACAAGAGCTAAGTC
ATCCAAATATAATTGGCCGCCTTGATGCTTTTGGATGTAAGTCTAATATTAGCCTTGTCTTTGGTTTTATGGAAACTGAT
CTAGAGGTTATAATAAAGGATAATAGTCTTGTGCTGACAACATCACACATCAAAGCCTGCATGTTGATGACTCTTCAAGG
ATTAGAATATTTACATCAACATTGGATCCTACATAGGGATCTGAAACCAAGCAACTTGTTGCTAGATGAAAATGGAGTTC
TAAAACTGGCAGATTTTGGCCTGGCCAAATCATTTGGGAGCCCCAGTAGAGCTTATACATATCAGGTTGCAACCAGGTGG
TATCAGGCCCCTGAGTTACTATTTGGAGCTAGGATGTATGGTGTAGGTGTGGACATGTGGGCTGTTGGCTGTATATTAGC
AGAGTTACTTCTAAGGGTTCCTTTTTTGTCAGGAGATTCAGAGCTTGATCAGCTAACAAGAATATTT

Alignment

ORF - retro_ptro_1707 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.39 %
• Parental protein coverage: 60.4 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LGEGQFATVYKARDKNTNQIVAIKKIKLGHRSEAKDGINRTALREIKLLQELSHPNIIGLLDAFGHKSNI
          .G...FA.VYKARDKNTNQIVAIKKIKLGHRSEAKDGINRTALREI.LLQELSHPNIIG.LDAFG.KSNI
Retrocopy VGGFKFAVVYKARDKNTNQIVAIKKIKLGHRSEAKDGINRTALREIQLLQELSHPNIIGRLDAFGCKSNI

Parental  SLVFDFMETDLEVIIKDNSLVLTPSHIKAYMLMTLQGLEYLHQHWILHRDLKPNNLLLDENGVLKLADFG
          SLVF.FMETDLEVIIKDNSLVLT.SHIKA.MLMTLQGLEYLHQHWILHRDLKP.NLLLDENGVLKLADFG
Retrocopy SLVFGFMETDLEVIIKDNSLVLTTSHIKACMLMTLQGLEYLHQHWILHRDLKPSNLLLDENGVLKLADFG

Parental  LAKSFGSPNRAYTHQVVTRWYRAPELLFGARMYGVGVDMWAVGCILAELLLRVPFLPGDSDLDQLTRIF
          LAKSFGSP.RAYT.QV.TRWY.APELLFGARMYGVGVDMWAVGCILAELLLRVPFL.GDS.LDQLTRIF
Retrocopy LAKSFGSPSRAYTYQVATRWYQAPELLFGARMYGVGVDMWAVGCILAELLLRVPFLSGDSELDQLTRIF

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	9.47 RPM
SRP007412_cerebellum	0.00 RPM	11.18 RPM
SRP007412_heart	0.03 RPM	5.95 RPM
SRP007412_kidney	0.00 RPM	10.54 RPM
SRP007412_liver	0.00 RPM	9.89 RPM
SRP007412_testis	0.00 RPM	55.12 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1707 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1707 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1707 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2335
Gorilla gorilla	retro_ggor_1772
Pongo abelii	retro_pabe_2114

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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,