RetrogeneDB ID: retro_ptro_1984

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:49658084..49660036(+)
• Located in intron of: ENSPTRG00000023807

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZNF341
• Ensembl ID: ENSPTRG00000013406
• Aliases: None
• Description: Zinc finger protein 341 [Source:UniProtKB/TrEMBL;Acc:K7BAD8]

Sequence

>retro_ptro_1984
GGCCCCCCTGGGCATCCCAATCCTGGTGGGAATGGTGTGGTGAAGGTGTACAGTGCTGCTGCACTCGTGGCTGGGAGTGG
AATGGTGGAGATCCAGGCACTGGGGATGCAGCCCTACCCACCCCTGGAGGTGCCAAACCAGTGTGTGGAGGCTCCAGTAT
ACCCCACCCCCGCAGTGTACAGCCCTGGCAAACAGGGATTCACACCCAAAGGACCAAACCCTGCTGCCCCATGACCAGTG
CCACCGGGGGCACTGTGGCCACCTTTGACTCTCCACCAATGCTGAAGACCCCACGGGCTAAACGTACCAGGGGACTCCTG
GAAGCTACAGGGAAGCCAAAGGCTCAGAAACTCAAGTGCCCATACTGTGACAAGTCATTCACCAAAAACTTCGACCTGCA
GCAGCACATCTGAAGCCACACAGGTGAGAAGCCCTTCCAATGCATTGCGTGTGGCCGTGCCTTTGCCCAGAAGTCTAATG
TTAAGAAACACATGCAGACCCACAAGGTATGGCCTTCAGGACACGGTGGTGGCACTGTGTCTCGAAACTCTGTGACTGTA
CAGGTCTTGGCCCTGAACCCCAGCAGGCAGGAGGATGAGGAAAACACAGGGTTGGGCCAGCCCCTACCAAGCTTGCCACA
GCTCCAGGCCTGGCCCACAGCCAGCGATGGCAAGGGGCAAGCCGGAAACCCAAGCAGGTAGTCCTCATCTACAGCTCCTA
CTTGTTCCAGTTCTGCCCCAGCAAGTTCAGCACCTATTTCCAGCTCAAGTCTCACATGACCCAGCATAAGAACTAGCAGG
TGCACAAATGTGTGGTCAAAAGCTGTGCCCAGACGTTCCCAAAGCTCGACACATTTCTGGAGCACATCAAGAGCCACCAG
GAGGAGCTGAGCTACCCCGGCCACTTCTGCAACAAGGACTTACCCCTGCTATACGACCTGAGCGTGCACCAGTACTCCCA
CAGCCTCCTTCCACAGCACAGCCCCAAGAAGGGCGGTGCCGTCTACAAGTGTGTCAAACGTGTCAACAAATATCCACCCC
GGAGGCCCTGGAGCATCACCTGCAGACCGCCACTCACAACTTCCCCTGCCCACACTGCTAGAAGGTGTTTCCTTGTGAAC
GCTACCTGCAGCGTCATCTGCCAACCCACTGCAGCGGGGGCAGGTTCAAGGGCCAGGTGTGCAAGAAGTCCTCCCGGCGG
GTGCATTACCTCAAACTGCGCGCGCACAACCACTCAGGCGAGAAGCCCTACAAATGCTCGGTGTGCGAGTCCGCATTCAA
CCGCAAGGACAAACTGTGAGAGAGACATGTTGATCCACCAGCTCTTCAAGAAATACAAATGCCCTTTATCGACGCACACA
GGCTGCGGTAAGTTGTTCAACCGGCCGGACAAGCTGAAGGCCCATGTCCTCTCCCACTCCGGCACGAAGCTCCACAAATG
CGCCCTGTGCAGCCGTGCCCACCTCGCCGAGCACCTGCGCGCCCACACGGGCTACTACAAGTTCCGCTGTGCTGGCTGTG
CCAAGGACTTTTTCCGCCACAAATACCTCAAAGATCACCGCTGTCGTCTCGGCCCCCAGAAGGAAAAGGACCTGCAAACC
CGGCGGCACTCCCCCGCCCCACCACAGCCCGCGAGAAGAGGGCAGCCCCGCGCCGTGGCGGCAGTGGTGGGCGCAAGGTG
GTGACCCCCTTGCCTGACCCGCTGGGGCTGGAGGAGATGAAGGACACAGGGGCTGGTCTGGTGCCCGAGGCCGTCCCGGG
CAAGCCGCCCTTCGCAGAGCTGAACGCGGAGCTTTCCGTCGTCGTGGGTGGTGCGGTGGGCACGGAATCTGAGCTGGTGG
TACCTGGACAGCTGAGGGGCTGGGCTCCAACCTGGCTCTGGCAGGGCTGCAGGCCGGGGCCGAGGGCCCATGTGCCATGC
TCGCTGTGCTCATCTACATCGAGGCCTCAGAG

Alignment

ORF - retro_ptro_1984 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.65 %
• Parental protein coverage: 76.11 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  GPPGRPNPGGNGVVEVYSAAAPLAGSGTVEIQALGMQPYPPLEVPNQCVEPPVYPTPTVYSPGKQGFKPK
          GPPG.PNPGGNGVV.VYSAAA..AGSG.VEIQALGMQPYPPLEVPNQCVE.PVYPTP.VYSPGKQGF.PK
Retrocopy GPPGHPNPGGNGVVKVYSAAALVAGSGMVEIQALGMQPYPPLEVPNQCVEAPVYPTPAVYSPGKQGFTPK

Parental  GPNPAAP-MTSATGGTVATFDSPATLKTRRAKGARGLPEAAGKPKAQKLKCSYCDKSFTKNFDLQQHIRS
          GPNPAAP.MTSATGGTVATFDSP..LKT.RAK..RGL.EA.GKPKAQKLKC.YCDKSFTKNFDLQQHI.S
Retrocopy GPNPAAP<MTSATGGTVATFDSPPMLKTPRAKRTRGLLEATGKPKAQKLKCPYCDKSFTKNFDLQQHI*S

Parental  HTGEKPFQCIACGRAFAQKSNVKKHMQTHKVWPPGHSGGTVSRNSVTVQVMALNPSRQEDEESTGLGQPL
          HTGEKPFQCIACGRAFAQKSNVKKHMQTHKVWP.GH.GGTVSRNSVTVQV.ALNPSRQEDEE.TGLGQPL
Retrocopy HTGEKPFQCIACGRAFAQKSNVKKHMQTHKVWPSGHGGGTVSRNSVTVQVLALNPSRQEDEENTGLGQPL

Parental  PGAPQPQALSTAGEEEGD-KPEPKQVVLIDSSYLCQFCPSKFSTYFQLKSHMTQHKNEQVYKCVVKSCAQ
          P..PQ.QA..TA....G.....PKQVVLI.SSYL.QFCPSKFSTYFQLKSHMTQHKN.QV.KCVVKSCAQ
Retrocopy PSLPQLQAWPTASDGKGQ<SRKPKQVVLIYSSYLFQFCPSKFSTYFQLKSHMTQHKN*QVHKCVVKSCAQ

Parental  TFPKLDTFLEHIKSHQEELSYRCHLCGKDFPSLYDLGVHQYSHSLLPQHSPKKDNAVYKCVKCVNKY-ST
          TFPKLDTFLEHIKSHQEELSY..H.C.KD.P.LYDL.VHQYSHSLLPQHSPKK..AVYKCVK.VNKY.ST
Retrocopy TFPKLDTFLEHIKSHQEELSYPGHFCNKDLPLLYDLSVHQYSHSLLPQHSPKKGGAVYKCVKRVNKY<ST

Parental  PEALEHHLQTATHNFPCPHCQKVFPCERYLRRHLPTHGSGGRFKCQVCKKFFRREHYLKLHAHIHSGEKP
          PEALEHHLQTATHNFPCPHC.KVFPCERYL.RHLPTH.SGGRFK.QVCKK..RR.HYLKL.AH.HSGEKP
Retrocopy PEALEHHLQTATHNFPCPHC*KVFPCERYLQRHLPTHCSGGRFKGQVCKKSSRRVHYLKLRAHNHSGEKP

Parental  YKCSVCESAFNRKDKL-KRHMLIHEPFKKYKCPFSTHTGCSKEFNRPDKLKAHILSHSGMKLHKCALCSK
          YKCSVCESAFNRKDKL..R.MLIH..FKKYKCP.STHTGC.K.FNRPDKLKAH.LSHSG.KLHKCALCS.
Retrocopy YKCSVCESAFNRKDKL>ERDMLIHQLFKKYKCPLSTHTGCGKLFNRPDKLKAHVLSHSGTKLHKCALCSR

Parental  SFSRRAHLAEHQRAHTGNYKFRCAGCAKGFSRHKYLKDHRCRLGPQKDKDLQTRR----PPQ--RRAAPR
          ......HL..H....TG.YKFRCAGCAK.F.RHKYLKDHRCRLGPQK.KDLQTRR....PPQ..RR..PR
Retrocopy AHLAE-HLRAH----TGYYKFRCAGCAKDFFRHKYLKDHRCRLGPQKEKDLQTRRHSPAPPQPARRGQPR

Parental  SC-GSGG-RKVLTPLPDPLGLEELKDTGAGLVPEAVPGKPPFAEPDAVLSIVVGGAVGAEPELVVPGH-A
          ...G..G.RKV.TPLPDPLGLEE.KDTGAGLVPEAVPGKPPFAE..A.LS.VVGGAVG.E.ELVVPG..A
Retrocopy AV<GGSGGRKVVTPLPDPLGLEEMKDTGAGLVPEAVPGKPPFAELNAELSVVVGGAVGTESELVVPGQ<A

Parental  EGLGSNLALAELQAGAEGPCAMLAVPVYIQASE
          EGLGSNLALA.LQAGAEGPCAMLAV..YI.ASE
Retrocopy EGLGSNLALAGLQAGAEGPCAMLAVLIYIEASE

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	0.02 RPM	12.19 RPM
SRP007412_cerebellum	0.14 RPM	9.64 RPM
SRP007412_heart	0.00 RPM	1.11 RPM
SRP007412_kidney	0.03 RPM	4.18 RPM
SRP007412_liver	0.00 RPM	2.85 RPM
SRP007412_testis	0.42 RPM	2.85 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1984 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1984 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1984 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000131061	1 retrocopy	retro_hsap_3057,
Nomascus leucogenys	ENSNLEG00000010013	1 retrocopy	retro_nleu_1651,
Pan troglodytes	ENSPTRG00000013406	1 retrocopy	retro_ptro_1984 ,