RetrogeneDB ID: retro_ptro_2482

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:130450728..130452324(-)
• Located in intron of: ENSPTRG00000018588

Retrocopy information

• Ensembl ID: ENSPTRG00000040684
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BMPR1A
• Ensembl ID: ENSPTRG00000002706
• Aliases: None
• Description: None

Sequence

>retro_ptro_2482
ATGACTCAGCTATACATTTACATCAGATTATTGGGAGCCTATTTGTTCATCATTTCTTGTGTTCAAGGACAGAATCTGGA
TAGTATGCTCCACGGCACTGGGATGAAATCAGACTCCGACCAGAAAAAGTCAGAAAATGGAGTAACCTTAGCACCAGAGG
ATACCTTGCCTTTTTTAAAGTGCTATTGCTCAGGGCACTGCCCAGATGATGCTATTAATAACACATGCATAACTAATGGA
CGTTGCTTTGCCATCATAGAAGAAGATGACCAGGGAGAAACCACATTAGCTTCAGGGTGTATGAAATATGAAGGATCTGA
TTTTCAGTGCAAAGATTCTCCAAAAGCCCAGCTACGCCGGACAATAGAATGTTGTCGGACCAATTTATGTAACCAGTATT
TGCAACCCACACTGCCCCCTGTTGTCATAGGTCCATTTTTTGATGGCAGCATTCGATGGCTGGTTTTGCTCATTTCTATG
GCTGTCTGCATAATTGCTATGATCATCTTCTCCAGCTGCTTTTGTTACAAACATTATTGCAAGAGCATCTCAAGCAGACG
TCGTTACAATCGTGATTTGGAACAGGATGAAGCATTTATTCCAGTTGGAGAATCACTAAAAGACCTTATTGACCAGTCAC
AAAGTTCTGGTAGTGGGTCTGGACTACCTTTATTGGTTCAGCGAACTATTGCCAAACAGATTCAGATGGTCCGGCAAGTT
GGTAAAGGCCGATATGGAGAAGTATGGATGGGCAAATGGCATGGCGAAAGAGTGGCGGTGAAAGTATTCTTTACCACTGA
AGAAGCCAGCTGGTTTCGAGAAACAGAAATCTACCAAACTGTGCTAATGCGCCATGAAAACATACTTGGTTTCATAGCGG
CAGATATTAAAGGTACAGGTTCCTTGACTCAGCTCTATTTGATTACTGATTACCATGAAAATGGATCTCTCTATGACTTC
CTGAAATGTGCTACACTGGACACCAGAGCCCTGCTTAAATTGGCTTATTCAGCTGCCTGTGGTCTGTGCCACCTGCACAC
AGAAATTTATGGCACCCAAGGAAAGCCCGCAATTGCTCATCGAGACCTAAAGAGCAAAAACATCCTCATCAAGAAAAATG
GGAGTTGCTGCATTGCTGACCTGGGCCTTGCTGTTAAATTCAACAGTGACACAAATGAAGTTGATGTGCCCTTGAATACC
AGGGTGGGCACCAAACGCTACATGGCTCCAGAAGTGCTGGACGAAAGCCTGAACAAAAACCACTTCCAGCCCTACATCAT
GGCTGGTATCTACAGCTTCGGCCTAATCATTTGGGAGATGGCTCGTCGTTGTATCACAGGAGGGATCGTGGAAGAGTACC
AATTGCCATATTATAACATGGTACCGAGTGATCCGTCATACGAAGATATGCATGAGGTTGTGTGTGTCAAACGTTTGCGG
CCAATTGTGTCTAATCGGTGGAACAGTGATGAATGTCTACGAGCAGTTTTGAAGCTAATGTCAGAATGCTGGGCCCACAA
TCCAGCCTCCAGACTCACAGCATTGAGAATTAAGAAGACGCTTGCCAAGATGGTTGAATCCCAAGATGTAAAAATC

Alignment

ORF - retro_ptro_2482 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.5 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTQLYIYIRLLGAYLFIISRVQGQNLDSMLHGTGMKSDSNQKKSENGVTLAPEDTLPFLKCYCSGHCPDD
          MTQLYIYIRLLGAYLFIIS.VQGQNLDSMLHGTGMKSDS.QKKSENGVTLAPEDTLPFLKCYCSGHCPDD
Retrocopy MTQLYIYIRLLGAYLFIISCVQGQNLDSMLHGTGMKSDSDQKKSENGVTLAPEDTLPFLKCYCSGHCPDD

Parental  AINNTCITNGHCFAIIEEDDQGETTLASGCMKYEGSDFQCKDSPKAQLRRTIECCRTNLCNQYLQPTLPP
          AINNTCITNG.CFAIIEEDDQGETTLASGCMKYEGSDFQCKDSPKAQLRRTIECCRTNLCNQYLQPTLPP
Retrocopy AINNTCITNGRCFAIIEEDDQGETTLASGCMKYEGSDFQCKDSPKAQLRRTIECCRTNLCNQYLQPTLPP

Parental  VVIGPFFDGSIRWLVLLISMAVCIIAMIIFSSCFCYKHYCKSISSRRRYNRDLEQDEAFIPVGESLKDLI
          VVIGPFFDGSIRWLVLLISMAVCIIAMIIFSSCFCYKHYCKSISSRRRYNRDLEQDEAFIPVGESLKDLI
Retrocopy VVIGPFFDGSIRWLVLLISMAVCIIAMIIFSSCFCYKHYCKSISSRRRYNRDLEQDEAFIPVGESLKDLI

Parental  DQSQSSGSGSGLPLLVQRTIAKQIQMVRQVGKGRYGEVWMGKWRGEKVAVKVFFTTEEASWFRETEIYQT
          DQSQSSGSGSGLPLLVQRTIAKQIQMVRQVGKGRYGEVWMGKW.GE.VAVKVFFTTEEASWFRETEIYQT
Retrocopy DQSQSSGSGSGLPLLVQRTIAKQIQMVRQVGKGRYGEVWMGKWHGERVAVKVFFTTEEASWFRETEIYQT

Parental  VLMRHENILGFIAADIKGTGSWTQLYLITDYHENGSLYDFLKCATLDTRALLKLAYSAACGLCHLHTEIY
          VLMRHENILGFIAADIKGTGS.TQLYLITDYHENGSLYDFLKCATLDTRALLKLAYSAACGLCHLHTEIY
Retrocopy VLMRHENILGFIAADIKGTGSLTQLYLITDYHENGSLYDFLKCATLDTRALLKLAYSAACGLCHLHTEIY

Parental  GTQGKPAIAHRDLKSKNILIKKNGSCCIADLGLAVKFNSDTNEVDVPLNTRVGTKRYMAPEVLDESLNKN
          GTQGKPAIAHRDLKSKNILIKKNGSCCIADLGLAVKFNSDTNEVDVPLNTRVGTKRYMAPEVLDESLNKN
Retrocopy GTQGKPAIAHRDLKSKNILIKKNGSCCIADLGLAVKFNSDTNEVDVPLNTRVGTKRYMAPEVLDESLNKN

Parental  HFQPYIMADIYSFGLIIWEMARRCITGGIVEEYQLPYYNMVPSDPSYEDMREVVCVKRLRPIVSNRWNSD
          HFQPYIMA.IYSFGLIIWEMARRCITGGIVEEYQLPYYNMVPSDPSYEDM.EVVCVKRLRPIVSNRWNSD
Retrocopy HFQPYIMAGIYSFGLIIWEMARRCITGGIVEEYQLPYYNMVPSDPSYEDMHEVVCVKRLRPIVSNRWNSD

Parental  ECLRAVLKLMSECWAHNPASRLTALRIKKTLAKMVESQDVKI
          ECLRAVLKLMSECWAHNPASRLTALRIKKTLAKMVESQDVKI
Retrocopy ECLRAVLKLMSECWAHNPASRLTALRIKKTLAKMVESQDVKI

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	0.50 RPM	8.01 RPM
SRP007412_cerebellum	0.18 RPM	10.68 RPM
SRP007412_heart	0.50 RPM	16.76 RPM
SRP007412_kidney	0.37 RPM	16.19 RPM
SRP007412_liver	0.10 RPM	5.11 RPM
SRP007412_testis	0.11 RPM	9.80 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2482 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2482 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2482 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3659
Gorilla gorilla	retro_ggor_2471

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000107779	2 retrocopies	retro_hsap_3659, retro_hsap_934,
Gorilla gorilla	ENSGGOG00000003720	1 retrocopy	retro_ggor_2471,
Pan troglodytes	ENSPTRG00000002706	1 retrocopy	retro_ptro_2482 ,
Rattus norvegicus	ENSRNOG00000010814	1 retrocopy	retro_rnor_2707,