RetrogeneDB ID: retro_ptro_344

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:135364353..135365888(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000039658
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SMU1
• Ensembl ID: ENSPTRG00000020853
• Aliases: None
• Description: None

Sequence

>retro_ptro_344
ATGTTGATCAAAATTGAATCTTCGGATGTGATCCACCTTATCATGCAGTACTTGAAGGAGAACAGTTTACATCAGGCATT
AGCCACCTTGCAGGAGGAGACTACTGTGTCTCTGAATACTGTGGACAGCATTGAGAGTTTTGTGGCTGACATTAACAGTG
GCCATTGGGATACTGTGTTGCAGGCTATACAGTCTCTGAAATTGCCAGACAAAACCCTCATTGACCTCTATGAACAGATT
GTTCTGGAATTGATAGAGCTCCGTGAATTGGGTGCTGCCAGGTCACTATTGAGACAGACTGATCCCATGATCATGTTAAA
ACAAACACAGCCAGAGCAATATATTCATCTGGAGAACCTTTTGGCCAGGTCTTACTTTGATCCTCGTGAGGCATACCCAG
ATGGAAGTAGCAAAGAAAAGAGAAGAGCAGCAATTGCCCAGGCCTTGGCTGGTGAAGTCAGTGTGGTGCCTCCATCTCGT
CTCATGGCACTGCTGGGACAGGCACTGAAGTGGCAGCAGCATCAGGGATTGCTTCCTCCTGGTATGACCATAGATTTGTT
TTGAGGCAAAGCAGCTGTCAAAGATGTGGAAGAAGAAAAGTTTCCTACACAACTGAGCAGGCATATTAAGTTTGGTCAGA
AATCACAAGTGGAGTGTGCTCGATTTTCCCCAGATGGTCAGTATTTGGTCACTGGGTCTGTTGATGGACTCACTGAAGTA
TGGAACTTTACTACTAGAAAAATCAGAAAGGATCTTAAGTACCAGGCCCAGGATAACTTTATGATGATGGATGATGCTGT
CCTCTGCATGTGTTTCAGCAGAGATACAGAAATGTTAGCAAATGGGGCCCAAGATGGAAAAATCAAGGTATGGAAGATTC
AGAGCAGACAATATTTAAGGAGATATGAGAGGGCACACAGTAAGGGTGTCACGTGTCTAAGCTTTTCTGAGGATAGCAGT
CAGATCCTTAGTGCTTCTTTTGACCAGACAATTAGAATTCATGGTTTAAAATCTGGGAAAACCCTGAAGGAATTTTGTAG
CCATTCCTCCTTTGTTAACAAAGCAACATTTACACAAGATGGACATTATATTATTAGTGCATCCTCTGATGGCACTGTAA
AGATCTGGAATATGAAGACCACAGAATGTTCAAATACCTTTAAATCCCTGGGCAGCACTGCAGGGACAGATATTACTGTC
AACAGTGTGATTCTACTTCCTAAAAATCCTGAGCACTTTGTGGTGTGCAACAGATCAAACACAGTGGTCATCATGAACAT
GCAGGGGCAGATTGTCAGAAACTTCAGTTCTGGTAAAAGAGAAGGTGGGGACTTTTCTGTGCCCTCTCTCCCCGTGGTGA
ATGGATCTACTGTGTAGGGGAGGACTTTGTGCTCTACTGTTTCAGTACAGCCACTGGCAAACTGGAGAGAACTTTGACAG
TGCACAAGAAGGATGTGATTGGTATTGCACATCACCCTCATCAGAACCTGATTGCTACCTACAGTGAAGATGGACTCCTA
AAGCTCTGGAAACCA

Alignment

ORF - retro_ptro_344 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.14 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSIEIESSDVIRLIMQYLKENSLHRALATLQEETTVSLNTVDSIESFVADINSGHWDTVLQAIQSLKLPD
          M.I.IESSDVI.LIMQYLKENSLH.ALATLQEETTVSLNTVDSIESFVADINSGHWDTVLQAIQSLKLPD
Retrocopy MLIKIESSDVIHLIMQYLKENSLHQALATLQEETTVSLNTVDSIESFVADINSGHWDTVLQAIQSLKLPD

Parental  KTLIDLYEQVVLELIELRELGAARSLLRQTDPMIMLKQTQPERYIHLENLLARSYFDPREAYPDGSSKEK
          KTLIDLYEQ.VLELIELRELGAARSLLRQTDPMIMLKQTQPE.YIHLENLLARSYFDPREAYPDGSSKEK
Retrocopy KTLIDLYEQIVLELIELRELGAARSLLRQTDPMIMLKQTQPEQYIHLENLLARSYFDPREAYPDGSSKEK

Parental  RRAAIAQALAGEVSVVPPSRLMALLGQALKWQQHQGLLPPGMTIDLFRGKAAVKDVEEEKFPTQLSRHIK
          RRAAIAQALAGEVSVVPPSRLMALLGQALKWQQHQGLLPPGMTIDLF.GKAAVKDVEEEKFPTQLSRHIK
Retrocopy RRAAIAQALAGEVSVVPPSRLMALLGQALKWQQHQGLLPPGMTIDLF*GKAAVKDVEEEKFPTQLSRHIK

Parental  FGQKSHVECARFSPDGQYLVTGSVDGFIEVWNFTTGKIRKDLKYQAQDNFMMMDDAVLCMCFSRDTEMLA
          FGQKS.VECARFSPDGQYLVTGSVDG..EVWNFTT.KIRKDLKYQAQDNFMMMDDAVLCMCFSRDTEMLA
Retrocopy FGQKSQVECARFSPDGQYLVTGSVDGLTEVWNFTTRKIRKDLKYQAQDNFMMMDDAVLCMCFSRDTEMLA

Parental  TGAQDGKIKVWKIQSGQCLRRFERAHSKGVTCLSFSKDSSQILSASFDQTIRIHGLKSGKTLKEFRGHSS
          .GAQDGKIKVWKIQS.Q.LRR.ERAHSKGVTCLSFS.DSSQILSASFDQTIRIHGLKSGKTLKEF..HSS
Retrocopy NGAQDGKIKVWKIQSRQYLRRYERAHSKGVTCLSFSEDSSQILSASFDQTIRIHGLKSGKTLKEFCSHSS

Parental  FVNEATFTQDGHYIISASSDGTVKIWNMKTTECSNTFKSLGSTAGTDITVNSVILLPKNPEHFVVCNRSN
          FVN.ATFTQDGHYIISASSDGTVKIWNMKTTECSNTFKSLGSTAGTDITVNSVILLPKNPEHFVVCNRSN
Retrocopy FVNKATFTQDGHYIISASSDGTVKIWNMKTTECSNTFKSLGSTAGTDITVNSVILLPKNPEHFVVCNRSN

Parental  TVVIMNMQGQIVRSFSSGKREGGDF-VCCALSPRGEWIYCVGEDFVLYCFSTVTGKLERTLTVHEKDVIG
          TVVIMNMQGQIVR.FSSGKREGGDF..C.ALSPRGEWIYCVGEDFVLYCFST.TGKLERTLTVH.KDVIG
Retrocopy TVVIMNMQGQIVRNFSSGKREGGDF<FC-ALSPRGEWIYCVGEDFVLYCFSTATGKLERTLTVHKKDVIG

Parental  IAHHPHQNLIATYSEDGLLKLWKP
          IAHHPHQNLIATYSEDGLLKLWKP
Retrocopy IAHHPHQNLIATYSEDGLLKLWKP

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	0.25 RPM	20.63 RPM
SRP007412_cerebellum	0.32 RPM	33.41 RPM
SRP007412_heart	0.17 RPM	22.30 RPM
SRP007412_kidney	0.39 RPM	22.07 RPM
SRP007412_liver	0.23 RPM	19.61 RPM
SRP007412_testis	0.32 RPM	42.79 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_344 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_344 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_344 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_457
Gorilla gorilla	retro_ggor_440
Pongo abelii	retro_pabe_274

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000006212	1 retrocopy	retro_cpor_819,
Homo sapiens	ENSG00000122692	1 retrocopy	retro_hsap_457,
Gorilla gorilla	ENSGGOG00000014802	1 retrocopy	retro_ggor_440,
Myotis lucifugus	ENSMLUG00000016097	1 retrocopy	retro_mluc_213,
Monodelphis domestica	ENSMODG00000003439	1 retrocopy	retro_mdom_965,
Ochotona princeps	ENSOPRG00000011389	2 retrocopies	retro_opri_19, retro_opri_741,
Pongo abelii	ENSPPYG00000019140	1 retrocopy	retro_pabe_274,
Pan troglodytes	ENSPTRG00000008551	1 retrocopy	retro_ptro_1569,
Pan troglodytes	ENSPTRG00000020853	1 retrocopy	retro_ptro_344 ,
Pan troglodytes	ENSPTRG00000023653	2 retrocopies	retro_ptro_18, retro_ptro_1975,