RetrogeneDB ID: retro_pabe_1757

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1_random:15170209..15171483(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ELL2
• Ensembl ID: ENSPPYG00000015647
• Aliases: None
• Description: elongation factor, RNA polymerase II, 2 [Source:HGNC Symbol;Acc:17064]

Sequence

>retro_pabe_1757
TATGGGCTCTCGTTCGGACGGCTGGGGCAGGACAACATCACCGTACTGCATGTGAAGCTCACCGAGTCGGCGATCCAGGC
GCTCCAGACTTACCAGAGCCACAAGAATTTAATTCCTTTTCGACCTTCAATTCATTTCGAAAGACTCCAGGAGCTTGTCA
AAATTCCCAAAAATGATTCCCTCAATGAAGTTCATAACTTTAACTTTTATTTGTCAAATGTGGGCAAAGACAACCCTCAG
GGCAGCTTTGACTGCGTCCAGCAAACATTCTCCAGCTCTGGAGCCTCCCAGCTCAATTGGCTGGGATTTATACAAGATAA
AATTACAGTGTGTGCAACAAACGACTGGGATCAGATGACACGAGAAAGAATGACCCAGGCCGAGGAGGAATCCCGCAACC
GAAGCACAAAAGTTATCAAACCCGGTGGACCACATGTAGGAAAAAGAGTGCAAATTCGGAAAGCACCTCAAGCTGTTTCA
GATACAGTTCCTGAGAGGAAAAGGTCAACCCCCATGAACCCTGCAAATACAATTCGATAGACACACAGCAGCAGCAGCGT
CTCTCAGAGGCCATACGGGGACAGGGTGGTTCACTTACTGGCCCTGAAGGCCTACAAGAAACCGGAGCTACTTGCTAGAC
TCCAGAAAGATGGTGTCAATCAAAAAGACAGGAACTCCTTGGGAGCAACTCTGCAACAGGTAGCCAATCTGAATCCTAAG
GACCTCTCATATACCTTAAAGGATTATGTTTTTAAAGAGCTTCAAAGAGACTGGCCTGGATACAGTGAAATAGACAGACA
GTCATTGGAGTCAGTGCTCTCTAGAAAACTAAATCCATCTCAGAATGCTGCAGGCACCAGCTGTTCAGAATCTCCTGTGT
ATTCTAGTAGAGACGCTGTATCTTCTCCTCAGAAACGGCTTTTGGATTCAGAGTTTATTGATCCTTTAATGAATAAAAAA
GCCCGAATATCTCACCTGACGAACAGAGTACCACCAACACTAAATGGTCATTTGAATCCCACCAGTGAAAAATCTGCTGC
AGGCCTCCCGCTGCCCGCTGCGGCTGCTGCCATCCCCACCTCTCCACCACTTGCCTTCAACCCATCTGCCTGTTTCACAT
CCTCCTCAGATTGTAAATTCTAACTCCAATTCCCCTAGCACTCCAGTAAGGCTGGGGGACTCAGACCTACCTGTTGACAG
TTTTAGTCAAAACGATAGTATCTATGAGACCAGCAAGACAATATACCTCTAGGACTTCTCTGGAAACTTACCCC

Alignment

ORF - retro_pabe_1757 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.89 %
• Parental protein coverage: 66.41 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  YGLSCGRLGQDNITVLHVKLTETAIRALETYQSHKNLIPFRPSIQFQGLHGLVKIPKNDPLNEVHNFNFY
          YGLS.GRLGQDNITVLHVKLTE.AI.AL.TYQSHKNLIPFRPSI.F..L..LVKIPKND.LNEVHNFNFY
Retrocopy YGLSFGRLGQDNITVLHVKLTESAIQALQTYQSHKNLIPFRPSIHFERLQELVKIPKNDSLNEVHNFNFY

Parental  LSNVGKDNPQGSFDCIQQTFSSSGASQLNCLGFIQDKITVCATNDSYQMTRERMTQAEEESRNRSTKVIK
          LSNVGKDNPQGSFDC.QQTFSSSGASQLN.LGFIQDKITVCATND..QMTRERMTQAEEESRNRSTKVIK
Retrocopy LSNVGKDNPQGSFDCVQQTFSSSGASQLNWLGFIQDKITVCATNDWDQMTRERMTQAEEESRNRSTKVIK

Parental  PGGPYVGKRVQIRKAPQAVSDTVPERKRSTPMNPANTIRKTHSSSTVSQRPYRDRVIHLLALKAYKKPEL
          PGGP.VGKRVQIRKAPQAVSDTVPERKRSTPMNPANTIR.THSSS.VSQRPY.DRV.HLLALKAYKKPEL
Retrocopy PGGPHVGKRVQIRKAPQAVSDTVPERKRSTPMNPANTIR*THSSSSVSQRPYGDRVVHLLALKAYKKPEL

Parental  LARLQKDGVNQKDKNSLGAILQQVANLNPKDLSYTLKDYVFKELQRDWPGYSEIDRRSLESVLSRKLNPS
          LARLQKDGVNQKD.NSLGA.LQQVANLNPKDLSYTLKDYVFKELQRDWPGYSEIDR.SLESVLSRKLNPS
Retrocopy LARLQKDGVNQKDRNSLGATLQQVANLNPKDLSYTLKDYVFKELQRDWPGYSEIDRQSLESVLSRKLNPS

Parental  QNAAGTSRSESPVCSSRDAVTSPQKRLLDSEFIDPLMNKKARISHLTNRVPPTLNGHLNPTSEKSAVGLP
          QNAAGTS.SESPV.SSRDAV.SPQKRLLDSEFIDPLMNKKARISHLTNRVPPTLNGHLNPTSEKSA.GLP
Retrocopy QNAAGTSCSESPVYSSRDAVSSPQKRLLDSEFIDPLMNKKARISHLTNRVPPTLNGHLNPTSEKSAAGLP

Parental  LPPAAAAIPTPPP-LPSTYLPVSHPPQIVNSNSNSPSTPEGRGTQDLPVDSFSQNDSIYE-DQQD-KYTS
          LP.AAAAIPT.PP.LPST.LPVSHPPQIVNSNSNSPSTP...G..DLPVDSFSQNDSIYE.DQQD..YTS
Retrocopy LPAAAAAIPTSPP>LPSTHLPVSHPPQIVNSNSNSPSTPVRLGDSDLPVDSFSQNDSIYE<DQQD<QYTS

Parental  RTSLETLP
          RTSLET.P
Retrocopy RTSLETYP

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	34.06 RPM
SRP007412_cerebellum	0.00 RPM	12.40 RPM
SRP007412_heart	0.00 RPM	24.62 RPM
SRP007412_kidney	0.00 RPM	26.35 RPM
SRP007412_liver	0.00 RPM	88.87 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1757 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1757 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1757 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,