RetrogeneDB ID: retro_ptro_1339

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 19:57730382..57731018(+)
• Located in intron of: ENSPTRG00000022655

Retrocopy information

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

Parental gene information

• Parental gene symbol: PABPN1
• Ensembl ID: ENSPTRG00000006168
• Aliases: None
• Description: poly(A) binding protein, nuclear 1 [Source:HGNC Symbol;Acc:8565]

Sequence

>retro_ptro_1339
AGCACTGGGCCTGCGGGCTGTCCGGGCTCCGGGCCGGGGCGGCGGCGCCATCTTGTGCCCGGGGCCGGTGGGGAGGCGGG
GGAGGTTGCCCCGGGGGGCGCAGGGGACCATGGGAACGGCCTGGAATCTGAGGAACTGGAGCCTGAGGAGCTGCTGTTGC
AGCCGGAGCCCGAAGAGGAGCCGCTCCAGCCCCGCGCCCCGTGCCTGGGAGCTCCAGGACCCGGGCCTCGTTCAGGAGCC
ACCGGCAGCCAAGAGGAGGGGGAGGAGCCGGGACCGGTCGAGGGTGACCCGGGGGACGGTGCCATTGAGGACCCGGTGCT
GGAAGCTATCAAAGCTGGAGTCAGGGAGGTGGACGAAGAAGCTGAGAAGCTAAAGGAGCTACAGAACGACGCAGAGAAGC
AGATGAATGTGAGTCTACCTCCAGGCAATGCTGGCCCAGTGATCACGTCCATTGAGGAGAAGATGGAGGCTGATGCCCGT
TCCATCAGTGCTGGCAATGGGGACTGCGGCGCAACAGCAGAAGAGCCGGAAGCTCACTTTCACGGCTGTGGTTCAGTCAA
CCATGTTACCATACTCTGTGACAAATTTAGTGGTCATCCCAAAGGGTTTGCATATATAGAGTTCTCAAAGAGTCAA

Alignment

ORF - retro_ptro_1339 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.41 %
• Parental protein coverage: 70.26 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAGAAGGRGSGPGRRRHLVPGAGGEAGEGAPGGAGDYGNGLESEELEPEELLLEPEPEPEPEEEPPRPRA
          ..G.AG..GSGPGRRRHLVPGAGGEAGE.APGGAGD.GNGLESEELEPEELLL.....PEPEEEP..PRA
Retrocopy STGPAGCPGSGPGRRRHLVPGAGGEAGEVAPGGAGDHGNGLESEELEPEELLL----QPEPEEEPLQPRA

Parental  PP-GAPGPGPGSGAPGSQEEEEEPGLVEGDPGDGAIEDPELEAIKARVREMEEEAEKLKELQNEVEKQMN
          P..GAPGPGP.SGA.GSQEE.EEPG.VEGDPGDGAIEDP.LEAIKA.VRE..EEAEKLKELQN..EKQMN
Retrocopy PCLGAPGPGPRSGATGSQEEGEEPGPVEGDPGDGAIEDPVLEAIKAGVREVDEEAEKLKELQNDAEKQMN

Parental  MSPPPGNAGPVIMSIEEKMEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYI
          .S.PPGNAGPVI.SIEEKMEADARSI..GN.D.GATAEE.EAHFHGCGSVN.VTILCDKFSGHPKGFAYI
Retrocopy VSLPPGNAGPVITSIEEKMEADARSISAGNGDCGATAEEPEAHFHGCGSVNHVTILCDKFSGHPKGFAYI

Parental  EFSDKE
          EFS...
Retrocopy EFSKSQ

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	0.57 RPM	158.83 RPM
SRP007412_cerebellum	1.83 RPM	166.73 RPM
SRP007412_heart	0.38 RPM	49.81 RPM
SRP007412_kidney	0.47 RPM	125.97 RPM
SRP007412_liver	0.03 RPM	90.58 RPM
SRP007412_testis	3.48 RPM	140.05 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1339 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1339 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1339 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006884	1 retrocopy	retro_btau_693,
Callithrix jacchus	ENSCJAG00000007960	4 retrocopies	retro_cjac_1263, retro_cjac_2291, retro_cjac_3278, retro_cjac_3836,
Dipodomys ordii	ENSDORG00000002873	1 retrocopy	retro_dord_606,
Homo sapiens	ENSG00000100836	1 retrocopy	retro_hsap_4855,
Gorilla gorilla	ENSGGOG00000022683	2 retrocopies	retro_ggor_1454, retro_ggor_3030,
Mustela putorius furo	ENSMPUG00000006775	1 retrocopy	retro_mputfur_496,
Mus musculus	ENSMUSG00000022194	1 retrocopy	retro_mmus_403,
Nomascus leucogenys	ENSNLEG00000015009	2 retrocopies	retro_nleu_2066, retro_nleu_3023,
Otolemur garnettii	ENSOGAG00000008710	1 retrocopy	retro_ogar_797,
Pongo abelii	ENSPPYG00000005663	2 retrocopies	retro_pabe_1645, retro_pabe_3773,
Pan troglodytes	ENSPTRG00000006168	2 retrocopies	retro_ptro_1339 , retro_ptro_3232,
Sus scrofa	ENSSSCG00000002023	1 retrocopy	retro_sscr_625,