RetrogeneDB ID: retro_ptro_1827

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:135888160..135889630(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: G2E3
• Ensembl ID: ENSPTRG00000006234
• Aliases: None
• Description: None

Sequence

>retro_ptro_1827
GTGGCTTGTGTTTTCTGTCGCAAAAAGGATGACTGTCCTAATAAATATGGAGAAAAGAAAACTAAGGAGAAATGGAATCT
CACTGTACATTATTATTCTTTGTTGATGTCAAGTGGAATTTGGCAGAGAGGTAAAGAAGGAGTTTATGGTTTTCTATTAG
AAGATACCAGGAAGGAAGTGAATAGAGCTTCTAAACTGAAATGCTGTCTTTGCAAGAAAAATGGTGCTTCAGTTGGATGT
GTTGCACCCTAATGTAAATGAAGTTATTTCCCATGTGGACTTCAGAGAGAATGTATTTTCCAGTTTATTGGCAATTTCAC
ATCATTTTGTTGGAACCATCGACCTGTTCAAATAATTACATCTAATAATTATAGAGACTCCTTACCATGCACCATTTGCT
CGGAATTTATTGAGCCTATTCTAAGTTATAACATATTACAAAGTGCTTGTTGTAAGAACGCTTGGTTTCATAGAGACTGT
TTACAGGTTCAAGCAATAAATGCAGGAGTGTTTTTCTTTAGGTGTACAATATGCAATAATAGTGACATCTTTCAGAAAGA
GATGTTGAGAATGGGAATTCATATTCCTGAAAAAGATGCATCCTGGGAATTAGAGGAAAATGCTTATCAAGAGCTTCTGC
AGCACTATGAGCATTGTGATGTTCAAAAATGTCATTGCAAAGAAGGGTGAGACTATAATGCACCTGATAGCAAATGGGAA
ATAAAGCGCTGTCAGTGTTGTGGTTCCAGTGACACACACTTAGCCTGCTCTTCACTACGGTCATGGGAACAAAATTGGGA
GTTTTGGGAATGTAGGGGTATTATCTACAGTTCAGGAGTGTTCCAGAAAGCCAAAAACATGTATTATCCAACTCTAATAA
TGTGGGGATTACAGATTGTTGGAAGAGTCATCACCTAAATTACCCAGACAGTCACCTGTATTCCAGAGTAAAGATCTACT
GAGGCAAGGCAGCAAATTTAGAAGGAATGTATCAACACTATTAATGAGTTAGGATTCCAAATTTAAAAAAAAACTACAAG
ATTATGTATCAACAAAGCCAATATCTGAAATCGTGCCTTAGATGGATTCAGAAATCAAAACTTTAATCCTTCATATGCAA
TTGAAGTAGCATATGTTATTGAAAATGATAATTTTGGAAGTGGACATCCTGGATCAAAGCAAGAATTTCTGAGTGTCTTA
ATGCAACATCTTGAGAACTCATCATTGTTTGAGGGGTCCTTGTCAAAGAACTTATCTCTAAATTCTCAAGCTCTGAAAGG
GAATCTTTACTATGAAGCTGGCAAAATGCTTGCCATTTATTTAGTTCACGGTGGTCCTTCACCTGGTTTCTTTTCTAAAA
CCTTGTTTAACTGCCTTGTTTATGGACCAAAAAATACCCAGCCAATTTTAGATGATGTTTCAGACTTTGATGTGGCACAG
ATTATAATCAGGATAAATACTGCAACAACA

Alignment

ORF - retro_ptro_1827 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.55 %
• Parental protein coverage: 70.11 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LACVFCRKNDDCPNKYGEKKTKEKWNLTVHYYCLLMSSGIWQRGKEEEGVYGFLIEDIRKEVNRASKLKC
          .ACVFCRK.DDCPNKYGEKKTKEKWNLTVHYY.LLMSSGIWQRGKE..GVYGFL.ED.RKEVNRASKLKC
Retrocopy VACVFCRKKDDCPNKYGEKKTKEKWNLTVHYYSLLMSSGIWQRGKE--GVYGFLLEDTRKEVNRASKLKC

Parental  CVCKKNGASIGCVAPRCKRSYHFPCGLQRECIFQFTGNFASFCWDHRPVQIITSNNYRESLPCTICLEFI
          C.CKKNGAS.GCVAP.CK.SY.FPCGLQRECIFQF.GNF.SFCW.HRPVQIITSNNYR.SLPCTIC.EFI
Retrocopy CLCKKNGASVGCVAP*CK*SY-FPCGLQRECIFQFIGNFTSFCWNHRPVQIITSNNYRDSLPCTICSEFI

Parental  EPIPSYNVLRSPCCKNAWFHRDCLQVQAINAGVFFFRCTICNNSDIFQKEMLRMGIHIPEKDASWELEEN
          EPI.SYN.L.S.CCKNAWFHRDCLQVQAINAGVFFFRCTICNNSDIFQKEMLRMGIHIPEKDASWELEEN
Retrocopy EPILSYNILQSACCKNAWFHRDCLQVQAINAGVFFFRCTICNNSDIFQKEMLRMGIHIPEKDASWELEEN

Parental  AYQELLQHYERCDVRRCRCKEGRDYNAPDSKWEIKRCHCCGSSGTHLACSSLRSWEQNWECLECRGIIYN
          AYQELLQHYE.CDV..C.CKEG.DYNAPDSKWEIKRC.CCGSS.THLACSSLRSWEQNWE..ECRGIIY.
Retrocopy AYQELLQHYEHCDVQKCHCKEG*DYNAPDSKWEIKRCQCCGSSDTHLACSSLRSWEQNWEFWECRGIIYS

Parental  SGEFQKAK-KHVLPNSNNVGITDC-LLEESSPKLPRQSPGSQSKDLLRQGSKFRRNVSTLLI-ELGFQIK
          SG.FQKAK.KHVL.NSNNVGITDC.L.E.S.PKLPRQSP..QSKDLLRQGSKFRRNVSTLL..ELGFQI.
Retrocopy SGVFQKAK<KHVLSNSNNVGITDC<LEESS-PKLPRQSPVFQSKDLLRQGSKFRRNVSTLLM<ELGFQIX

Parental  KKTKRLYINKANIWNSALDAFRNRNFNPSYAIEVAYVIENDNFGSEHPGSKQEFLSLLMQHLENSSLFEG
          ....RL.INKANI.N.ALD.FRN.NFNPSYAIEVAYVIENDNFGS.HPGSKQEFLS.LMQHLENSSLFEG
Retrocopy XXXTRLCINKANI*NRALDGFRNQNFNPSYAIEVAYVIENDNFGSGHPGSKQEFLSVLMQHLENSSLFEG

Parental  SLSKNLSLNSQALKENLYYEAGKMLAISLVHGGPSPGFFSKTLFNCLVYGPENTQPILDDVSDFDVAQII
          SLSKNLSLNSQALK.NLYYEAGKMLAI.LVHGGPSPGFFSKTLFNCLVYGP.NTQPILDDVSDFDVAQII
Retrocopy SLSKNLSLNSQALKGNLYYEAGKMLAIYLVHGGPSPGFFSKTLFNCLVYGPKNTQPILDDVSDFDVAQII

Parental  IRINTATT
          IRINTATT
Retrocopy IRINTATT

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	6.92 RPM
SRP007412_cerebellum	0.00 RPM	12.87 RPM
SRP007412_heart	0.00 RPM	4.37 RPM
SRP007412_kidney	0.03 RPM	7.22 RPM
SRP007412_liver	0.00 RPM	3.14 RPM
SRP007412_testis	0.00 RPM	114.87 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1827 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1827 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1827 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2706

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002109	1 retrocopy	retro_chof_341,
Homo sapiens	ENSG00000092140	1 retrocopy	retro_hsap_2706,
Pongo abelii	ENSPPYG00000005719	1 retrocopy	retro_pabe_144,
Pan troglodytes	ENSPTRG00000006234	1 retrocopy	retro_ptro_1827 ,