RetrogeneDB ID: retro_ptro_3039

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: GL392075.1:5669480..5670709(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SMARCE1
• Ensembl ID: ENSPTRG00000022902
• Aliases: None
• Description: None

Sequence

>retro_ptro_3039
ATGTCAAAAAGACCATCTTATGCCCCACCTCCCACCCCAGCTCCTGCAACACAAATGCTCAGCACACCAGGGTTTGTGGG
ATACCATCCATACAGTCAGCTCGCCGACAGCAACTACAGGCTGGGAGGAAACCCGCCCACCAACAGCCGGGTCAGGGCAT
CCTCCGCTATTACCATTCCAAAACCCTGAAAGCCAGCAGATAAGCTGCTGATGCCCTACATGAGGTACAGCAGAAAGATC
TGAGACCAAATAAAGGCTTCCAACCCTGACCTAAAGTTGTGGGAGATTGGCTAGATTATTGGTGGCATGTGGCAAGATCT
CACTGATGAAAAACAAGAATATTTAAACGAATACAAAGCAGAAAAGATAGAGTACAATGAATCTATGAAGGCCTATCATA
ATTCCCCCGTGTACTTTGCTTACATAAATGCAAAAAGTCGTGCAGAAGCTGCTTTAGAGGGAGAAAGTGGACAGAGACAG
TCTCGCTTGGAGAAAGGAGAACCGTACATGAGCATTCAGCCTGCTGAAGATCCAGATGATTATGATGATGGCTTTTCAAT
GAAGCATACAGTCACTACCCATTTCCAGAGAAACTACCTCCTCATCAGTGAAATCCTTAGTGGGAGTGTGGTGGCAGACG
TTCGGTCAGTTGTCACAACAGCTAGAATGCAGGTCCTCGAACGACAGGTCCAGTCCTTAATGGTTCATCAGCGAAAACTA
GAAGCTGAACTTCTTCAAATAGAGGAACGACACCAGGAGAAGAAGAGGAAATTCCTGGAAAGCACAGATTCACTTAACAA
TGAACTTAAAAGGTTGTGCCGTCTGAAAGTAGAAGTGGATATGGAGAAAATGGCAGCTGAGATTGCACAGGCAGAGGAAC
AGGCCCGCAAAGGGCAGGAGGAAAGGGAGAAGGAGGCAGCAGAGCAAGCTGAGCGCAGTCAGAGCAGCATCCTTCCTGAG
GAAGAACAAGCAGCCAACAAAGGCGAGGAGAAGAAAGAAGACGACAACATTCCAATGGAGACAGAGGAGACACACCTTGA
AGAAATGACAGAGAGCCAACAGAATGGTGAAGAAGGCACGTCTACTCCTGAGGACAAGGAGAGTGGCAGGAGGGGGTGGA
CAGTATGGCAGAGGAAGGAACCAGGGATAGTAACACTGGCTCAGAGAGCAACAGCCCAACAGTGGAGGAGCCACCAACAG
ATCCCATACCAGAAGATGGGAAAAAACAA

Alignment

ORF - retro_ptro_3039 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.32 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSKRPSYAPPPTPAPATQMPSTPGFVGYNPYSHLAYNNYRLGGNPGTNSRVTASSGITIPKPPKPPDKPL
          MSKRPSYAPPPTPAPATQM.STPGFVGY.PYS.LA..NYRLGGNP.TNSRV.ASS.ITIPKP.KP.DK.L
Retrocopy MSKRPSYAPPPTPAPATQMLSTPGFVGYHPYSQLADSNYRLGGNPPTNSRVRASSAITIPKP*KPADKLL

Parental  MPYMRYSRKVWDQVKASNPDLKLWEIGKIIGGMWRDLTDEEKQEYLNEYEAEKIEYNESMKAYHNSPAYL
          MPYMRYSRK..DQ.KASNPDLKLWEIG.IIGGMW.DLTDE.KQEYLNEY.AEKIEYNESMKAYHNSP.Y.
Retrocopy MPYMRYSRKI*DQIKASNPDLKLWEIG*IIGGMWQDLTDE-KQEYLNEYKAEKIEYNESMKAYHNSPVYF

Parental  AYINAKSRAEAALEEESRQRQSRMEKGEPYMSIQPAEDPDDYDDGFSMKHTATARFQRNHRLISEILSES
          AYINAKSRAEAALE.ES.QRQSR.EKGEPYMSIQPAEDPDDYDDGFSMKHT.T..FQRN..LISEILS.S
Retrocopy AYINAKSRAEAALEGESGQRQSRLEKGEPYMSIQPAEDPDDYDDGFSMKHTVTTHFQRNYLLISEILSGS

Parental  VVPDVRSVVTTARMQVLKRQVQSLMVHQRKLEAELLQIEERHQEKKRKFLESTDSFNNELKRLCGLKVEV
          VV.DVRSVVTTARMQVL.RQVQSLMVHQRKLEAELLQIEERHQEKKRKFLESTDS.NNELKRLC.LKVEV
Retrocopy VVADVRSVVTTARMQVLERQVQSLMVHQRKLEAELLQIEERHQEKKRKFLESTDSLNNELKRLCRLKVEV

Parental  DMEKIAAEIAQAEEQARKRQEEREKEAAEQAERSQSSIVPEEEQAANKGEEKKDDENIPMETEETHLEET
          DMEK.AAEIAQAEEQARK.QEEREKEAAEQAERSQSSI.PEEEQAANKGEEKK.D.NIPMETEETHLEE.
Retrocopy DMEKMAAEIAQAEEQARKGQEEREKEAAEQAERSQSSILPEEEQAANKGEEKKEDDNIPMETEETHLEEM

Parental  TESQQNGEEGTSTPEDKESG-QEGVDSMAEEGTSDSNTGSESNSATVEEPPTDPIPEDEKKE
          TESQQNGEEGTSTPEDKESG.QEGVDSMAEEGT.DSNTGSESNS.TVEEPPTDPIPED.KK.
Retrocopy TESQQNGEEGTSTPEDKESG<QEGVDSMAEEGTRDSNTGSESNSPTVEEPPTDPIPEDGKKQ

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	2.25 RPM	27.08 RPM
SRP007412_cerebellum	0.72 RPM	47.28 RPM
SRP007412_heart	0.15 RPM	54.65 RPM
SRP007412_kidney	0.58 RPM	72.94 RPM
SRP007412_liver	0.00 RPM	56.47 RPM
SRP007412_testis	2.42 RPM	104.96 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3039 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3039 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3039 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1195
Gorilla gorilla	retro_ggor_931
Pongo abelii	retro_pabe_994
Macaca mulatta	retro_mmul_1284

---

Parental genes homology:

Parental genes homology involve 17 parental genes, and 68 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013573	4 retrocopies	retro_cjac_1107, retro_cjac_2109, retro_cjac_50, retro_cjac_854,
Homo sapiens	ENSG00000073584	5 retrocopies	retro_hsap_1195, retro_hsap_1304, retro_hsap_3623, retro_hsap_3947, retro_hsap_922,
Gorilla gorilla	ENSGGOG00000011803	2 retrocopies	retro_ggor_1020, retro_ggor_931,
Microcebus murinus	ENSMICG00000009821	4 retrocopies	retro_mmur_1408, retro_mmur_1592, retro_mmur_608, retro_mmur_928,
Myotis lucifugus	ENSMLUG00000004609	1 retrocopy	retro_mluc_1209,
Macaca mulatta	ENSMMUG00000004005	3 retrocopies	retro_mmul_1284, retro_mmul_2159, retro_mmul_2286,
Mustela putorius furo	ENSMPUG00000014660	4 retrocopies	retro_mputfur_1411, retro_mputfur_1482, retro_mputfur_1499, retro_mputfur_739,
Mus musculus	ENSMUSG00000037935	5 retrocopies	retro_mmus_1111, retro_mmus_1127, retro_mmus_2437, retro_mmus_2618, retro_mmus_3194,
Nomascus leucogenys	ENSNLEG00000001957	4 retrocopies	retro_nleu_1060, retro_nleu_2051, retro_nleu_2083, retro_nleu_286,
Oryctolagus cuniculus	ENSOCUG00000008981	1 retrocopy	retro_ocun_59,
Otolemur garnettii	ENSOGAG00000001652	7 retrocopies	retro_ogar_1734, retro_ogar_2059, retro_ogar_3199, retro_ogar_402, retro_ogar_454, retro_ogar_682, retro_ogar_760,
Ochotona princeps	ENSOPRG00000000985	1 retrocopy	retro_opri_731,
Pongo abelii	ENSPPYG00000008456	4 retrocopies	retro_pabe_2973, retro_pabe_3251, retro_pabe_794, retro_pabe_994,
Pan troglodytes	ENSPTRG00000022902	5 retrocopies	retro_ptro_2451, retro_ptro_2678, retro_ptro_3039 , retro_ptro_639, retro_ptro_894,
Pteropus vampyrus	ENSPVAG00000011355	1 retrocopy	retro_pvam_237,
Rattus norvegicus	ENSRNOG00000010676	7 retrocopies	retro_rnor_1278, retro_rnor_1311, retro_rnor_1456, retro_rnor_1507, retro_rnor_1599, retro_rnor_2383, retro_rnor_2593,
Tupaia belangeri	ENSTBEG00000000770	10 retrocopies	retro_tbel_1246, retro_tbel_1554, retro_tbel_2208, retro_tbel_2955, retro_tbel_4035, retro_tbel_4629, retro_tbel_4656, retro_tbel_658, retro_tbel_821, retro_tbel_844,