RetrogeneDB ID: retro_ptro_124

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:144570610..144573073(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000039915
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SMEK1
• Ensembl ID: ENSPTRG00000006638
• Aliases: None
• Description: None

Sequence

>retro_ptro_124
ATGACCGACACCCGGCGGCGGGTGAAGGTGTACACGCTCAACGAGGACCGGCAGCGGGACGACCGGGGCACCGGGCATGT
GTCGTCTGGCTACGTGGAGCGGCTGAAGGGCATGTCCCTGCTTGTCAGGGCTGAGAGCGACGGTTCTCTACTTTTAGAGT
CCAAAATAAATCCTAACACCGCATACCAGAAACAACAGGACACTCTGATTGTGTGGTCTGAAGCAGAAAATTATGACTTG
GCCCTTAGCTTTCAAGAAAAAGCTGGATGTGATGAAATTTGGGAGAAAATATGTCAGGTTCAAGGAAAGGACCCTTCCGT
GGACATCACTCAGGACCTTGTGGATGAATCTGAAGAGGAGCGTTTTGATGATATGTCATCGCCAGGCTTAGAATTGCCAT
CTTGTGAATTAAGTCGCCTTGAAGAAATTGCAGAACTTGTGGCATCATCTTTACCTTCACCTCTTCGTCGTGAAAAACTT
GCACTGGCACTAGAAAATGAGGGTTATATTAAAAAGCTCCTGGAGCTTTTTCATGTGTGTGAAGATTTGGAAAATATTGA
AGGACTGCACCACTTGTATGAAATTATCAAAGGCATCTTTCTCTTGAATCGAACTGCTCTTTTTGAAGTTATGTTCTCTG
AAGAATGTATAATGGACGTCATTGGATGTTTAGAATATGATCCTGCTTTATCACAACCACGAAAACACAGGGAATTTCTA
ACAAAAACAGCCAAGTTTAAAGAAGTGATTCCCATATCAGATCCTGAGCTGAAACAAAAAATTCATCAGACATACAGAGT
TCAGTATATACAAGATATGGTTCTACCAACTCCTTCGGTCTTTGAAGAAAACATGTTATCAACACTTCACTCTTTTATCT
TTTTCAATAAGGTAGAGATTGTTGGCATGTTGCAGGAAGATGAAAAATTTCTGACAGATTTGTTTGCACAACTAACAGAT
GAAGCAACAGATGAGGAAAAAAGACAGGAATTGGTTAACTTTTTAAAAGAATTTTGTGCGTTTTCCCAAACGCTACAGCC
TCAAAACAGAGATGCTTTTTTCAAGACTTTGTCAAACATGGGCATATTACCAGCTTTAGAAGTCATCCTTGGCATGGATG
ATACACAGGTGCGAAGTGCTGCTACTGATATGTTCTCATACTTGGTTGAATATAATCCATCCATGGTACGAGAGTTTGTC
ATGCAGGAGGCACAACAGAATGATGATGATATTTTGCTCATCAACCTCATTATAGAACATATGATTTGTGATACAGATCC
TGAACTTGGAGGAGCAGTCCAGCTTATGGGCCTGCTTCGAACTTTAGTTGACCCAGAGAACATGCTAGCCACTGCCAATA
AAACAGAAAAGACTGAATTTCTGGGTTTCTTCTACAAGCACTGTATGCATGTTCTCACTGCTCCTTTACTAGCAAATACA
ACAGAAGACAAACCTAGTAAAGATGATTTTCAGACTGCCCAACTATTGGCACTTGTATTGGAATTGTTAACATTTTGTGT
GGAGCACCATACCTACCACATAAAGAACTACATTATTAATAAGGATATCCTCCGGAGAGTGCTAGTTCTTATGGCCTCGA
AGCATGCTTTCTTGGCATTATGTGCCCTTCGTTTTAAAAGAAAGATTATTGGATTAAAAGATGAGTTTTACAACCGCTAC
ATAATGAAAAGTTTTTTGTTTGAACCAGTAGTGAAAGCATTTCTCAACAATGGATCCCGCTACAATCTGATGAACTCTGC
CATAATAGAGATGTTTGAATTTATTAGAGTGGAAGATATAAAATCATTAACTGCTCATGTAATTGAAAATTACTGGAAAG
CACTGGAAGATGTAGATTATGTACAGACATTTAAAGGATTAAAACTGAGATTTGAACAACAAAGAGAAAGGCAAGATAAT
CCCAAACTTGACAGTATGCGTTCCCTTTTGAGGAATCACAGATATCGAAGAGATGCCAGAACACTAGAAGATGAAGAAGA
GATGTGGTTTAACACAGATGAAGATGACATGGAAGATGGAGAAGCTGTAGTGTCTCCATCTGACAAAACTAAAAATGATG
ATGATATTATGGATCCAATAAGTAAATTCATGGAAAGGAAGAAATTAAAAGAAAGTGAGGAAAAGGAAGTGCTTCTGAAA
ACAAATCTTTCTGGACGGCAGAGCCCAAGTTTCAAGCTTTCCCTGTCCAGTGGAACGAAGACTAACCTCACCAGCCAGTC
ATCTACAACAAATCTGCCTGGTTCTCCGGGATCACCTGGATCCCCAGGATCTCCAGGCTCTCCTGGATCCGTACCTAAAA
ATACGTCTCAGACGGCAGCTATTACTACAAAGGGAGGCCTCGTGGGTCTGGTAGATTATCCTGATGATGATGATGATGAG
GATGAGGATGAAGATAAGGAAGATACGTTACCATTGTCAAAGAAAGCAAAATTTGATTCATAA

Alignment

ORF - retro_ptro_124 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.39 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTDTRRRVKVYTLNEDRQWDDRGTGHVSSGYVERLKGMSLLVRAESDGSLLLESKINPNTAYQKQQDTLI
          MTDTRRRVKVYTLNEDRQ.DDRGTGHVSSGYVERLKGMSLLVRAESDGSLLLESKINPNTAYQKQQDTLI
Retrocopy MTDTRRRVKVYTLNEDRQRDDRGTGHVSSGYVERLKGMSLLVRAESDGSLLLESKINPNTAYQKQQDTLI

Parental  VWSEAENYDLALSFQEKAGCDEIWEKICQVQGKDPSVDITQDLVDESEEERFDDMSSPGLELPSCELSRL
          VWSEAENYDLALSFQEKAGCDEIWEKICQVQGKDPSVDITQDLVDESEEERFDDMSSPGLELPSCELSRL
Retrocopy VWSEAENYDLALSFQEKAGCDEIWEKICQVQGKDPSVDITQDLVDESEEERFDDMSSPGLELPSCELSRL

Parental  EEIAELVASSLPSPLRREKLALALENEGYIKKLLELFHVCEDLENIEGLHHLYEIIKGIFLLNRTALFEV
          EEIAELVASSLPSPLRREKLALALENEGYIKKLLELFHVCEDLENIEGLHHLYEIIKGIFLLNRTALFEV
Retrocopy EEIAELVASSLPSPLRREKLALALENEGYIKKLLELFHVCEDLENIEGLHHLYEIIKGIFLLNRTALFEV

Parental  MFSEECIMDVIGCLEYDPALSQPRKHREFLTKTAKFKEVIPISDPELKQKIHQTYRVQYIQDMVLPTPSV
          MFSEECIMDVIGCLEYDPALSQPRKHREFLTKTAKFKEVIPISDPELKQKIHQTYRVQYIQDMVLPTPSV
Retrocopy MFSEECIMDVIGCLEYDPALSQPRKHREFLTKTAKFKEVIPISDPELKQKIHQTYRVQYIQDMVLPTPSV

Parental  FEENMLSTLHSFIFFNKVEIVGMLQEDEKFLTDLFAQLTDEATDEEKRQELVNFLKEFCAFSQTLQPQNR
          FEENMLSTLHSFIFFNKVEIVGMLQEDEKFLTDLFAQLTDEATDEEKRQELVNFLKEFCAFSQTLQPQNR
Retrocopy FEENMLSTLHSFIFFNKVEIVGMLQEDEKFLTDLFAQLTDEATDEEKRQELVNFLKEFCAFSQTLQPQNR

Parental  DAFFKTLSNMGILPALEVILGMDDTQVRSAATDIFSYLVEYNPSMVREFVMQEAQQNDDDILLINLIIEH
          DAFFKTLSNMGILPALEVILGMDDTQVRSAATD.FSYLVEYNPSMVREFVMQEAQQNDDDILLINLIIEH
Retrocopy DAFFKTLSNMGILPALEVILGMDDTQVRSAATDMFSYLVEYNPSMVREFVMQEAQQNDDDILLINLIIEH

Parental  MICDTDPELGGAVQLMGLLRTLVDPENMLATANKTEKTEFLGFFYKHCMHVLTAPLLANTTEDKPSKDDF
          MICDTDPELGGAVQLMGLLRTLVDPENMLATANKTEKTEFLGFFYKHCMHVLTAPLLANTTEDKPSKDDF
Retrocopy MICDTDPELGGAVQLMGLLRTLVDPENMLATANKTEKTEFLGFFYKHCMHVLTAPLLANTTEDKPSKDDF

Parental  QTAQLLALVLELLTFCVEHHTYHIKNYIINKDILRRVLVLMASKHAFLALCALRFKRKIIGLKDEFYNRY
          QTAQLLALVLELLTFCVEHHTYHIKNYIINKDILRRVLVLMASKHAFLALCALRFKRKIIGLKDEFYNRY
Retrocopy QTAQLLALVLELLTFCVEHHTYHIKNYIINKDILRRVLVLMASKHAFLALCALRFKRKIIGLKDEFYNRY

Parental  IMKSFLFEPVVKAFLNNGSRYNLMNSAIIEMFEFIRVEDIKSLTAHVIENYWKALEDVDYVQTFKGLKLR
          IMKSFLFEPVVKAFLNNGSRYNLMNSAIIEMFEFIRVEDIKSLTAHVIENYWKALEDVDYVQTFKGLKLR
Retrocopy IMKSFLFEPVVKAFLNNGSRYNLMNSAIIEMFEFIRVEDIKSLTAHVIENYWKALEDVDYVQTFKGLKLR

Parental  FEQQRERQDNPKLDSMRSILRNHRYRRDARTLEDEEEMWFNTDEDDMEDGEAVVSPSDKTKNDDDIMDPI
          FEQQRERQDNPKLDSMRS.LRNHRYRRDARTLEDEEEMWFNTDEDDMEDGEAVVSPSDKTKNDDDIMDPI
Retrocopy FEQQRERQDNPKLDSMRSLLRNHRYRRDARTLEDEEEMWFNTDEDDMEDGEAVVSPSDKTKNDDDIMDPI

Parental  SKFMERKKLKESEEKEVLLKTNLSGRQSPSFKLSLSSGTKTNLTSQSSTTNLPGSPGSPGSPGSPGSPGS
          SKFMERKKLKESEEKEVLLKTNLSGRQSPSFKLSLSSGTKTNLTSQSSTTNLPGSPGSPGSPGSPGSPGS
Retrocopy SKFMERKKLKESEEKEVLLKTNLSGRQSPSFKLSLSSGTKTNLTSQSSTTNLPGSPGSPGSPGSPGSPGS

Parental  VPKNTSQTAAITTKGGLVGLVDYPDDDEDDDEDEDKEDTLPLSKKAKFDS
          VPKNTSQTAAITTKGGLVGLVDYPDDD.D.DEDEDKEDTLPLSKKAKFDS
Retrocopy VPKNTSQTAAITTKGGLVGLVDYPDDDDDEDEDEDKEDTLPLSKKAKFDS

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	0.75 RPM	10.31 RPM
SRP007412_cerebellum	0.36 RPM	11.97 RPM
SRP007412_heart	0.20 RPM	5.51 RPM
SRP007412_kidney	0.26 RPM	11.45 RPM
SRP007412_liver	0.03 RPM	7.40 RPM
SRP007412_testis	2.32 RPM	35.62 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_124 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_124 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_124 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000012467	1 retrocopy	retro_dord_714,
Erinaceus europaeus	ENSEEUG00000006324	1 retrocopy	retro_eeur_316,
Pan troglodytes	ENSPTRG00000006638	1 retrocopy	retro_ptro_124 ,
Pan troglodytes	ENSPTRG00000011933	1 retrocopy	retro_ptro_3191,
Pteropus vampyrus	ENSPVAG00000015294	1 retrocopy	retro_pvam_1091,
Tupaia belangeri	ENSTBEG00000008535	1 retrocopy	retro_tbel_2368,
Tarsius syrichta	ENSTSYG00000010333	1 retrocopy	retro_tsyr_863,
Tursiops truncatus	ENSTTRG00000013598	1 retrocopy	retro_ttru_1398,
Vicugna pacos	ENSVPAG00000002765	1 retrocopy	retro_vpac_536,