RetrogeneDB ID: retro_ptro_55

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 17:22942152..22944405(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000039807
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TLK2
• Ensembl ID: ENSPTRG00000009506
• Aliases: None
• Description: None

Sequence

>retro_ptro_55
ATGATGGAAGAATTGCATAGCCTGGACCCACGACGGCAGAAATTATTGGAGGCCAGGTTTACTGGAGTAGGTGTTAGTAA
GGGACCACTTAATAGTGAGTCTTCCAACCAGAGCTTGTGCAGCGTCGGATCCTTGAGTGATAAAGAAGTAGAGACTCCCG
AGAAAAAGCAGAATGACCAGCGAAATCGGAAAAGAAAAGGTGAACCATATGAAACTAGCCAAGGGAAAGGCACTCCTAGG
GGACATAAAATTAGTGATTACTTTGAGTTTGCTGGGGGAAGCGGGCCAGGAACCAGCCCTGGCAGAAGTGTTCCACCAGT
TGCACGATCCTCACCGAAACATTCCTTATCCAGTCCCTTACCGCGACGAGTAGAACAGCCCCTCTATGGTTTAGATGGCA
GTGCTGCAAAGGAGGCAACGGAGGAGCAGTCTGCTCTGCCAACCCTCATGTCAGTGATGCTAGCAAAACCTCGGCTTGAC
ACAGAGCAGCTGGCGCAAAGGGGAGCTGGCCTCTGCTTCACTTTTGTTTCAGCTCAGCAAAACAGTCCCTCATCTACGGG
ATCTGGCAACACAGAGCATTCCTGCAGCTCCCAAAAACAGATCTCCATCCAGCACAGACAGACCCAGTCCGACCTCACAA
TAGAAAAAATATCTGCACTAGAAAACAGTAAGAATTCTGACTTAGAGAAGAAGGAGGGAAGAATAGATGATTTATTAAGA
GCCAACTGTGATTTGAGACGGCAGATTGATGAACAGCAAAAGATGCTAGAGAAATACAAGGAACGATTAAATAGATGTGT
GACAATGAGCAAGAAACTCCTTATAGAAAAGTCAAAACAAGAGAAGATGGCGTGTAGAGATAAGAGCATGCAAGACCGCT
TGAGACTGGGCCACTTTACTACTGTCCGACACGGAGCCTCATTTACTGAACAGTGGACAGATGGTTATGCTTTTCAGAAT
CTTATCAAGCAACAGGAAAGGATAAATTCACAGAGGGAAGAGATAGAAAGACAACGGAAAATGTTAGCAAAGCGGAAACC
TCCTGCCATGGGTCAGGCCCCTCCTGCAACCAATGAGCAGAAACAGCGGAAAAGCAAGACCAATGGAGCTGAAAATGAAA
CGTTAACGTTAGCAGAATACCATGAACAAGAAGAAATCTTCAAACTCAGATTAGGTCATCTTAAAAAGGAGGAAGCAGAG
ATCCAGGCAGAGCTGGAGAGGCTAGAAAGGGTTAGAAAGCTACATATCAGGGAACTAAAAAGGATACATAAAGAAGATAA
CTCACAATTTAAATATCATCCAACGCTAAGTGACAGATATTTGTTGTTACATCTTTTGGGTAGAGGAGGTTTCAGTGAAG
TTTACAAGGCATTTGATCTAACAGAGCAAAGATACGTAGCGGTGAAAATTCACCAGTTAAATAAAAACTGGAGAGATGAG
AAAAAGGAGAATTACCACAAGCATGCATGTAGGGAATACCGGATTCATAAAGAGCTGGATCATCCCAGAATAGTTAAGCT
GTATGATTACTTTTCACTGGATACTGACTCGTTTTGTACAGTATTAGAATACTGTGAGGGAAATGATCTGGACTTCTACC
TGAAACAGCACAAATTAATGTCGGAGAAAGAGGCCCGGTCCATTATCATGCAGACTGTGAATGCTTTAAAGTACTTAAAT
GAAATAAAACCTCCCATCATACACTATGACCTCAAACCAGGTAATATTCTTTTAGTAAATGGTACAGCATGTGGAGAGAT
AAAAATTACAGATTTTGGTCTTTCGAAGATCATGGATGATGATAGCTACAATTCAGTGGATGGCATGGAGCTAACATCAC
AAGGTGCTGGTACTTATTGGTATTTACCACCAGAGTGTTTTGTGGTTGGGAAAGAACCACCAAAGATCTCAAATAAAGTT
GATGTGTGGTCGGTGGGCATGATCTTCTATCAGTGTCTTTATGGAAGGAAGACTTTTGGCCATAACCAGTCTCAGCAAGA
CATCCTACAAGAGAATACGATTCTTAAAGCTACTGAAGTGCAGTTCCCACCAAAGCCAGTAGTAACACCTGAAGCAAAGG
CATTGATTCGACGATGCTTGGCCTACCGAAAGGAGGACCGCATTGATGTCCAGCAGCTGGCCTGTGATCCCTACTTGTTG
CCTCACATCCGAAAGTCAGTCTCTACGAGTAGCCCTGCTGGAGCTGCTATTGCATCAACCTCTGGGGCGTCCAATAACAG
TTCTTCTAATTGA

Alignment

ORF - retro_ptro_55 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.4 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MMEELHSLDPRRQELLEARFTGVGVSKGPLNSESSNQSLCSVGSLSDKEVETPEKKQNDQRNRKRKAEPY
          MMEELHSLDPRRQ.LLEARFTGVGVSKGPLNSESSNQSLCSVGSLSDKEVETPEKKQNDQRNRKRK.EPY
Retrocopy MMEELHSLDPRRQKLLEARFTGVGVSKGPLNSESSNQSLCSVGSLSDKEVETPEKKQNDQRNRKRKGEPY

Parental  ETSQGKGTPRGHKISDYFEFAGGSGPGTSPGRSVPPVARSSPQHSLSNPLPRRVEQPLYGLDGSAAKEAT
          ETSQGKGTPRGHKISDYFEFAGGSGPGTSPGRSVPPVARSSP.HSLS.PLPRRVEQPLYGLDGSAAKEAT
Retrocopy ETSQGKGTPRGHKISDYFEFAGGSGPGTSPGRSVPPVARSSPKHSLSSPLPRRVEQPLYGLDGSAAKEAT

Parental  EEQSALPTLMSVMLAKPRLDTEQLAQRGAGLCFTFVSAQQNSPSSTGSGNTEHSCSSQKQISIQHRQTQS
          EEQSALPTLMSVMLAKPRLDTEQLAQRGAGLCFTFVSAQQNSPSSTGSGNTEHSCSSQKQISIQHRQTQS
Retrocopy EEQSALPTLMSVMLAKPRLDTEQLAQRGAGLCFTFVSAQQNSPSSTGSGNTEHSCSSQKQISIQHRQTQS

Parental  DLTIEKISALENSKNSDLEKKEGRIDDLLRANCDLRRQIDEQQKMLEKYKERLNRCVTMSKKLLIEKSKQ
          DLTIEKISALENSKNSDLEKKEGRIDDLLRANCDLRRQIDEQQKMLEKYKERLNRCVTMSKKLLIEKSKQ
Retrocopy DLTIEKISALENSKNSDLEKKEGRIDDLLRANCDLRRQIDEQQKMLEKYKERLNRCVTMSKKLLIEKSKQ

Parental  EKMACRDKSMQDRLRLGHFTTVRHGASFTEQWTDGYAFQNLIKQQERINSQREEIERQRKMLAKRKPPAM
          EKMACRDKSMQDRLRLGHFTTVRHGASFTEQWTDGYAFQNLIKQQERINSQREEIERQRKMLAKRKPPAM
Retrocopy EKMACRDKSMQDRLRLGHFTTVRHGASFTEQWTDGYAFQNLIKQQERINSQREEIERQRKMLAKRKPPAM

Parental  GQAPPATNEQKQRKSKTNGAENETLTLAEYHEQEEIFKLRLGHLKKEEAEIQAELERLERVRNLHIRELK
          GQAPPATNEQKQRKSKTNGAENETLTLAEYHEQEEIFKLRLGHLKKEEAEIQAELERLERVR.LHIRELK
Retrocopy GQAPPATNEQKQRKSKTNGAENETLTLAEYHEQEEIFKLRLGHLKKEEAEIQAELERLERVRKLHIRELK

Parental  RIHNEDNSQFKDHPTLNDRYLLLHLLGRGGFSEVYKAFDLTEQRYVAVKIHQLNKNWRDEKKENYHKHAC
          RIH.EDNSQFK.HPTL.DRYLLLHLLGRGGFSEVYKAFDLTEQRYVAVKIHQLNKNWRDEKKENYHKHAC
Retrocopy RIHKEDNSQFKYHPTLSDRYLLLHLLGRGGFSEVYKAFDLTEQRYVAVKIHQLNKNWRDEKKENYHKHAC

Parental  REYRIHKELDHPRIVKLYDYFSLDTDSFCTVLEYCEGNDLDFYLKQHKLMSEKEARSIIMQIVNALKYLN
          REYRIHKELDHPRIVKLYDYFSLDTDSFCTVLEYCEGNDLDFYLKQHKLMSEKEARSIIMQ.VNALKYLN
Retrocopy REYRIHKELDHPRIVKLYDYFSLDTDSFCTVLEYCEGNDLDFYLKQHKLMSEKEARSIIMQTVNALKYLN

Parental  EIKPPIIHYDLKPGNILLVNGTACGEIKITDFGLSKIMDDDSYNSVDGMELTSQGAGTYWYLPPECFVVG
          EIKPPIIHYDLKPGNILLVNGTACGEIKITDFGLSKIMDDDSYNSVDGMELTSQGAGTYWYLPPECFVVG
Retrocopy EIKPPIIHYDLKPGNILLVNGTACGEIKITDFGLSKIMDDDSYNSVDGMELTSQGAGTYWYLPPECFVVG

Parental  KEPPKISNKVDVWSVGVIFYQCLYGRKPFGHNQSQQDILQENTILKATEVQFPPKPVVTPEAKAFIRRCL
          KEPPKISNKVDVWSVG.IFYQCLYGRK.FGHNQSQQDILQENTILKATEVQFPPKPVVTPEAKA.IRRCL
Retrocopy KEPPKISNKVDVWSVGMIFYQCLYGRKTFGHNQSQQDILQENTILKATEVQFPPKPVVTPEAKALIRRCL

Parental  AYRKEDRIDVQQLACDPYLLPHIRKSVSTSSPAGAAIASTSGASNNSSSN
          AYRKEDRIDVQQLACDPYLLPHIRKSVSTSSPAGAAIASTSGASNNSSSN
Retrocopy AYRKEDRIDVQQLACDPYLLPHIRKSVSTSSPAGAAIASTSGASNNSSSN

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	0.54 RPM	16.66 RPM
SRP007412_cerebellum	0.04 RPM	11.08 RPM
SRP007412_heart	0.09 RPM	10.67 RPM
SRP007412_kidney	0.05 RPM	11.06 RPM
SRP007412_liver	0.10 RPM	5.73 RPM
SRP007412_testis	1.48 RPM	76.30 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_55 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_55 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_55 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1823

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000146872	1 retrocopy	retro_hsap_1823,
Pan troglodytes	ENSPTRG00000009506	1 retrocopy	retro_ptro_55 ,