RetrogeneDB ID: retro_ptro_346

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:136495686..136497585(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ELL2
• Ensembl ID: ENSPTRG00000017090
• Aliases: None
• Description: None

Sequence

>retro_ptro_346
GGGGGCGGCGTCGCGGGGCAGCGCTATGGGCTCTCGTGCGGACGGCTGGGGCAGGACAACATCACCGTATTGCATGTGAA
GCTCACCGAGTCGGCGATCCAGGCGCTCCAGACTTACCAGAGCCACAAGAATTTAATTTCTTTTCGACCTTCAATTCAGT
TCCAAAGACTCCAGGAGCTTGTCAAAATTCCCAAAAATGATCCCCTCAATGAAGTTCATAACTTTAACTTTTATTTGTCA
AATGTGGGCAAAGACAACCCTCAGGGCAGCTTTGACTGCGTCCAGCAAACATTCTCCAGCTCTGGAGCCTCCCAGCTCAA
TTGCCTGGGATTTATACAAGATAAAATTACAGTGTGTGCAACAAACGACTCGGATCAGATGACACGAGAAAGAACGACCC
AGGCAGAGAAGGAATCCCGCAACCGAAGCACAAAAGTTATCAAACCCGGTGGACCATATGTAGGGAAAAGAGTGCAAATT
CGGAAAGCACCTCAAGCTGTTTCAGATACAGTTCCTGAGAGGAAAAGGTCAACCCCCATGAACCCTGCAAATACAATTCG
ATAGACACACAGCAGCAGCAGCGTCTCTCAGAGGCCATACAGGGATAGGGTGGTTCACTTACTGGCCCTGAAGGCCCACA
AGAAACCGGAGCTACTTGCTAGACTCCAGAAAGATGGTGTCAATCAAAAAGACAGGAACTCCCCGGGAGCAATTCTGCAA
CAGGTAGTCAATCTGAATCCTAAGGACCTCTCGTATACTTTAAAGGATTATGTTTTTAAAGAGCTTCAGGGAGACCAGCC
TGGATACAGTGAAATAGACAGATGGTCATTGGAGTCAATGCTCTCTAGAAAAGTAAATCTATCTCAGAATGCTGCAGGCA
CCAGCCGTTCAGAATCTCCAGTATGTTCTAGTAGAAACGCTGTATCTTCTCCTCAGAAACGGCTTTTGGATTCAGAGTTT
ATTGATCCTTTAATGGATAAAAAAGCCCGAATATCTCACCTGACGAACAGAGTACCACCAACACTAAATGGTCATTTGAA
TCCCACCAGTGAAAAATCTGCTGCAGGCCTCCCGCTGCCCCCTGCGGCTGCTGCCATCCCCACCCCTCCACCGCTTGCCT
TCAACCCATCTGCCCGTTTCACATCCTCCTCAGATTGTAAATTCTAACCCCAATTCCCCTAGCACTCCAGAAGGCCGGTG
GCTCAAGACCTACCTGTTGACAGTTTTAGTCAAAACGATAGTATCTATGAGAACCAGCAAGACAAATATACCTCTAGGAC
TTCTCTGGAAACCTTACCCCCTGGTTCAGTTCTATTAAAGTGTCCAAAGCCTATGGAAGAAAACCATTCAGTGTCTCACA
AAAAGTCCAAAAAGAAGTCTAAAAAACATAAGGAAAAGGACCAAATAAAAAAGCACGACATTGAGACTATTGAGGAAAAG
GAGAAAGATCTTAAGAGAGAAGAGGAAATTGCCAAGCTAAATAACTCCAGTCCAAATTCCAGTGGAGGAGTTAAAGAGGA
TTGCACTACCTCCATGGAACCTTCAGCAATTGAACTCCCAGATTATTTGATAAAATATATTGCTATCATCTCCTATGAGC
AACGCCGGAATTATAAAGATGACGTCAGTGCAGAGTATGATGAGTACAGAGCTTTGCATGCCAGGATGGAGACTGTAGCT
AGAAGATTTATCAAACTAGATGCACAAAGAAAGCGCCTTTCTCCAGGCTCAGAAGAGTATCAGAATGTTCATGAAGAAGT
CTTACAAGAATATCGGAAGATAAAGCAGTCTAGTCCCAGTTACCATGAAGAAAAATACAGATATGAATATCTTCATAACA
AGCTGGCTCACATCAAAAGGCTACTAGGTGAATTTGACCAACGGCAGGCAGAGTCATGG

Alignment

ORF - retro_ptro_346 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.13 %
• Parental protein coverage: 98.91 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GGLREEQRYGLSCGRLGQDNITVLHVKLTETAIRALETYQSHKNLIPFRPSIQFQGLHGLVKIPKNDPLN
          GG....QRYGLSCGRLGQDNITVLHVKLTE.AI.AL.TYQSHKNLI.FRPSIQFQ.L..LVKIPKNDPLN
Retrocopy GGGVAGQRYGLSCGRLGQDNITVLHVKLTESAIQALQTYQSHKNLISFRPSIQFQRLQELVKIPKNDPLN

Parental  EVHNFNFYLSNVGKDNPQGSFDCIQQTFSSSGASQLNCLGFIQDKITVCATNDSYQMTRERMTQAEEESR
          EVHNFNFYLSNVGKDNPQGSFDC.QQTFSSSGASQLNCLGFIQDKITVCATNDS.QMTRER.TQAE.ESR
Retrocopy EVHNFNFYLSNVGKDNPQGSFDCVQQTFSSSGASQLNCLGFIQDKITVCATNDSDQMTRERTTQAEKESR

Parental  NRSTKVIKPGGPYVGKRVQIRKAPQAVSDTVPERKRSTPMNPANTIRKTHSSSTVSQRPYRDRVIHLLAL
          NRSTKVIKPGGPYVGKRVQIRKAPQAVSDTVPERKRSTPMNPANTIR.THSSS.VSQRPYRDRV.HLLAL
Retrocopy NRSTKVIKPGGPYVGKRVQIRKAPQAVSDTVPERKRSTPMNPANTIR*THSSSSVSQRPYRDRVVHLLAL

Parental  KAYKKPELLARLQKDGVNQKDKNSLGAILQQVANLNSKDLSYTLKDYVFKELQRDWPGYSEIDRRSLESV
          KA.KKPELLARLQKDGVNQKD.NS.GAILQQV.NLN.KDLSYTLKDYVFKELQ.D.PGYSEIDR.SLES.
Retrocopy KAHKKPELLARLQKDGVNQKDRNSPGAILQQVVNLNPKDLSYTLKDYVFKELQGDQPGYSEIDRWSLESM

Parental  LSRKLNPSQNAAGTSHSESPVCSSRDAVSSPQKRLLDSEFIDPLMNKKARISHLTNRVPPTLNGHLNPTS
          LSRK.N.SQNAAGTS.SESPVCSSR.AVSSPQKRLLDSEFIDPLM.KKARISHLTNRVPPTLNGHLNPTS
Retrocopy LSRKVNLSQNAAGTSRSESPVCSSRNAVSSPQKRLLDSEFIDPLMDKKARISHLTNRVPPTLNGHLNPTS

Parental  EKSAAGLPLPPAAAAIPTPPP-LPSTYLPISHPPQIVNSNSNSPSTPEGRG-TQDLPVDSFSQNDSIYED
          EKSAAGLPLPPAAAAIPTPPP.LPST.LP.SHPPQIVNSN.NSPSTPEGR...QDLPVDSFSQNDSIYE.
Retrocopy EKSAAGLPLPPAAAAIPTPPP>LPSTHLPVSHPPQIVNSNPNSPSTPEGRW<AQDLPVDSFSQNDSIYEN

Parental  QQDKYTSRTSLETLPPGSVLLKCPKPMEENHSMSHKKSKKKSKKHKEKDQIKKHDIETIEEKEEDLKREE
          QQDKYTSRTSLETLPPGSVLLKCPKPMEENHS.SH................KKHDIETIEEKE.DLKREE
Retrocopy QQDKYTSRTSLETLPPGSVLLKCPKPMEENHSVSHXXXXXXXXXXXXXXXXKKHDIETIEEKEKDLKREE

Parental  EIAKLNNSSPNSSGGVKEDCTASMEPSAIELPDYLIKYIAIVSYEQRQNYKDDFNAEYDEYRALHARMET
          EIAKLNNSSPNSSGGVKEDCT.SMEPSAIELPDYLIKYIAI.SYEQR.NYKDD..AEYDEYRALHARMET
Retrocopy EIAKLNNSSPNSSGGVKEDCTTSMEPSAIELPDYLIKYIAIISYEQRRNYKDDVSAEYDEYRALHARMET

Parental  VARRFIKLDAQRKRLSPGSKEYQNVHEEVLQEYQKIKQSSPNYHEEKYRCEYLHNKLAHIKRLIGEFDQQ
          VARRFIKLDAQRKRLSPGS.EYQNVHEEVLQEY.KIKQSSP.YHEEKYR.EYLHNKLAHIKRL.GEFDQ.
Retrocopy VARRFIKLDAQRKRLSPGSEEYQNVHEEVLQEYRKIKQSSPSYHEEKYRYEYLHNKLAHIKRLLGEFDQR

Parental  QAESW
          QAESW
Retrocopy QAESW

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	0.11 RPM	39.65 RPM
SRP007412_cerebellum	0.04 RPM	13.62 RPM
SRP007412_heart	0.00 RPM	10.67 RPM
SRP007412_kidney	0.05 RPM	25.94 RPM
SRP007412_liver	0.03 RPM	59.48 RPM
SRP007412_testis	0.63 RPM	31.72 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_346 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_346 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_346 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010607	1 retrocopy	retro_amel_651,
Dasypus novemcinctus	ENSDNOG00000005103	1 retrocopy	retro_dnov_1413,
Equus caballus	ENSECAG00000022933	1 retrocopy	retro_ecab_1092,
Homo sapiens	ENSG00000118985	1 retrocopy	retro_hsap_459,
Nomascus leucogenys	ENSNLEG00000014192	1 retrocopy	retro_nleu_881,
Pongo abelii	ENSPPYG00000015647	1 retrocopy	retro_pabe_1757,
Pan troglodytes	ENSPTRG00000017090	1 retrocopy	retro_ptro_346 ,