RetrogeneDB ID: retro_ptro_2670

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 8:4705591..4706864(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PAICS
• Ensembl ID: ENSPTRG00000016081
• Aliases: None
• Description: None

Sequence

>retro_ptro_2670
ATGGCGACAGCTGAGGTACTGAACACTGGTAAAAAATTGTATGAGGGTAAAACAAAAGAAGTCTACGAATTGTTAGATAG
TCCAGGAAAAGTCCTCCTGCAGTCCAAGGACAAGATTACAGCAGGAAATGTAGCTGGAAAAAATCACCTGGAAGAAAAAG
TTGCAATCTCAAATAAAATCACCAGTTGTATTTTTCAGTTACTATAGGAAGCAGGTATTAAAACTACTTTCACCAGAAAA
TGTGGGGAGACAGCTTTCATTGCACCCCAGTGTGAAATGATTCCAACTGAATGGGTTTGCAGAAGAATAGCAACTGGTTC
TTTTCTCAAAAGAAATCCTGGTGTCAAGGAAGGATATAAGTTTACCCACCTAAAGTGGAGTTGTTTTTCAAGGATGCTGC
CAATAATGACCCACAGTGTTCTGAGGAACAGCTGATTGCTGCAAAATTTTGCTTTGCTGGACTTGTTATAGGCCAGACTG
AACTGGATATCATGAGTCATGCTACACAGGCTATATTTGAAATACTGGAGAAATCCTGGTTGCCCCAGAATTGTACACTG
GTTGATATGAAGATTGAATTTGGTGTTGATGTAACCACAAAGAAATTGTTCTTGCTGACGTTATTGACAATGATTCCTGG
AGACTCTGGCCATCAGGAGATCGAAGCCAACAGAAAGACAAACAGTCTTATCGGGACCTCAAAGAAGTAACTCCTTAAGG
GCTCCAAATGGTAAAGAAAAACTTTGAGTGGGTTGCAGAGAGAGTAGAGTTGCTTTTGAAATCAGAAAGTCAGTGCAGGG
TTGTAGTGTTGATGGGCTCTGCTTCTGATCTTGGTCACTGTGAAAAAATCAAGAAGGCCTGTGGAAATTTTGGCATTTCA
TGTGAACTTTGAGTAACATCTGCACATAAAGGACCAGATGAAACTCTGAGGATTAAAGCTGAGTATGAAGGGGATGGCAT
TCCTACTGTATTTGTGGCAGTGGCAGGCAGAAGTAATGGTTTGGGACCAGCGATGTCTGGGAACACTGCATATCCAGTTA
TCAGCTGTCCTCCCCTCACAGCAGACTGGGGAACTCAGGATGTGTGGTCTTCTCTTCGACTACCCAGTGGTCTTGGCTGT
TCAACCACACTTTCTCCAGAAGGATCAGCTCAATTTGCTGCTCAGATATTTGGGTTAAACAATCATTTGGTATAGAGCAA
ACTGTGAGCAAGCATTTTGAACACATGGATTTCCTTGAAGCAGGCTGACAAGAAAATCAGAGAATGTAATTTA

Alignment

ORF - retro_ptro_2670 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.68 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MATAEVLNIGKKLYEGKTKEVYELLDSPGKVLLQSKDQITAGNAARKNHLEGKAAISNKITSCIFRLLQE
          MATAEVLN.GKKLYEGKTKEVYELLDSPGKVLLQSKD.ITAGN.A.KNHLE.K.AISNKITSCIF.LL.E
Retrocopy MATAEVLNTGKKLYEGKTKEVYELLDSPGKVLLQSKDKITAGNVAGKNHLEEKVAISNKITSCIFQLL*E

Parental  AGIKTAFTRKCGETAFIAPQCEMIPIEWVCRRIATGSFLKRNPGVKEGYKF-YPPKVELFFKDDANNDPQ
          AGIKT.FTRKCGETAFIAPQCEMIP.EWVCRRIATGSFLKRNPGVKEGYKF.YPPKVELFFKD.ANNDPQ
Retrocopy AGIKTTFTRKCGETAFIAPQCEMIPTEWVCRRIATGSFLKRNPGVKEGYKF<YPPKVELFFKDAANNDPQ

Parental  WSEEQLIAAKFCFAGLVIGQTEVDIMSHATQAIFEILEKSWLPQNCTLVDMKIEFGVDVTT-KEIVLADV
          .SEEQLIAAKFCFAGLVIGQTE.DIMSHATQAIFEILEKSWLPQNCTLVDMKIEFGVDVTT.KEIVLADV
Retrocopy CSEEQLIAAKFCFAGLVIGQTELDIMSHATQAIFEILEKSWLPQNCTLVDMKIEFGVDVTT<KEIVLADV

Parental  IDNDSWRLWPSGDRSQQKDKQSYRDLKEVTPEGLQMVKKNFEWVAERVELLLKSESQCRVVVLMGSTSDL
          IDNDSWRLWPSGDRSQQKDKQSYRDLKEVTP.GLQMVKKNFEWVAERVELLLKSESQCRVVVLMGS.SDL
Retrocopy IDNDSWRLWPSGDRSQQKDKQSYRDLKEVTP*GLQMVKKNFEWVAERVELLLKSESQCRVVVLMGSASDL

Parental  GHCEKIKKACGSFGIPCELRVTSAHKGPDETLRIKAEYEGDGIPTVFVAVAGRSNGLGPVMSGNTAYPVI
          GHCEKIKKACG.FGI.CEL.VTSAHKGPDETLRIKAEYEGDGIPTVFVAVAGRSNGLGP.MSGNTAYPVI
Retrocopy GHCEKIKKACGNFGISCEL*VTSAHKGPDETLRIKAEYEGDGIPTVFVAVAGRSNGLGPAMSGNTAYPVI

Parental  SCPPLTPDWGAQDVWSSLRLPSGLGCSTILSPEGSAQFAAQIFGLSNHLVWSKLRASILNTWISLKQADK
          SCPPLT.DWG.QDVWSSLRLPSGLGCST.LSPEGSAQFAAQIFGL.NHLV.SKL.ASILNTWISLKQADK
Retrocopy SCPPLTADWGTQDVWSSLRLPSGLGCSTTLSPEGSAQFAAQIFGLNNHLV*SKL*ASILNTWISLKQADK

Parental  KIRECNL
          KIRECNL
Retrocopy KIRECNL

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	0.09 RPM	29.65 RPM
SRP007412_cerebellum	0.04 RPM	43.59 RPM
SRP007412_heart	0.00 RPM	15.51 RPM
SRP007412_kidney	0.00 RPM	38.65 RPM
SRP007412_liver	0.13 RPM	69.36 RPM
SRP007412_testis	0.00 RPM	34.78 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2670 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2670 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2670 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3927
Gorilla gorilla	retro_ggor_2643

---

Parental genes homology:

Parental genes homology involve 15 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010577	1 retrocopy	retro_btau_508,
Cavia porcellus	ENSCPOG00000010749	1 retrocopy	retro_cpor_969,
Dasypus novemcinctus	ENSDNOG00000013413	1 retrocopy	retro_dnov_284,
Echinops telfairi	ENSETEG00000015242	2 retrocopies	retro_etel_1918, retro_etel_341,
Homo sapiens	ENSG00000128050	3 retrocopies	retro_hsap_3802, retro_hsap_3915, retro_hsap_3927,
Gorilla gorilla	ENSGGOG00000024392	1 retrocopy	retro_ggor_2643,
Mus musculus	ENSMUSG00000029247	6 retrocopies	retro_mmus_1748, retro_mmus_2750, retro_mmus_2858, retro_mmus_3126, retro_mmus_653, retro_mmus_971,
Nomascus leucogenys	ENSNLEG00000008786	2 retrocopies	retro_nleu_1274, retro_nleu_2156,
Otolemur garnettii	ENSOGAG00000003575	2 retrocopies	retro_ogar_2138, retro_ogar_865,
Procavia capensis	ENSPCAG00000008531	1 retrocopy	retro_pcap_172,
Pan troglodytes	ENSPTRG00000016081	2 retrocopies	retro_ptro_2662, retro_ptro_2670 ,
Rattus norvegicus	ENSRNOG00000002101	3 retrocopies	retro_rnor_1891, retro_rnor_2768, retro_rnor_804,
Tupaia belangeri	ENSTBEG00000006751	1 retrocopy	retro_tbel_3697,
Tarsius syrichta	ENSTSYG00000010497	2 retrocopies	retro_tsyr_2170, retro_tsyr_329,
Drosophila melanogaster	FBgn0020513	1 retrocopy	retro_dmel_82,