RetrogeneDB ID: retro_ptro_1411

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 20:3361893..3362882(-)
• Located in intron of: ENSPTRG00000013198

Retrocopy information

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

Parental gene information

• Parental gene symbol: SF3A3
• Ensembl ID: ENSPTRG00000000559
• Aliases: None
• Description: Pan troglodytes splicing factor 3a, subunit 3, 60kDa (SF3A3), mRNA. [Source:RefSeq mRNA;Acc:NM_001246453]

Sequence

>retro_ptro_1411
ATGGAGACAATACCGGAGCAGCAGCGGCGCTATCATGAGGAGAAGGGAAGGCTCATGGACGTCATGGCCAAAGAGATGCT
CACTAAGAAGTCCACGCTCAATTCTGATCACCGCGCTCAGGCCATGCAAGATAGGTATATGGAGGTCAGTGGGAACCTGA
GGGATCTGTATGATGATAAAGATGGATTATGAAAGGAGGAACTCAATGCCATTTCAGGACCCAATGAGTTTGCTGAATTC
TATAATAGACTTGAGTAAATAAAGGAATTCCACCAGAAGCATCCAAATGAGATCTGTGTGCCAATGTCAGTGGAATTTGA
GGAGCTCCTGAAGGCTCAGACAATCCAAGTGAAGAGGCACAAAACTTGGTGGAGTTCACAGATGAAGAGGGATATGGTCG
TTACCTCGATCTCCGTGACTGTTACCTCAAGTACATTAACGTGAAGGCATCTGAGAAGCTGGATTATATTACATACCTGT
CCATCTCTGACCAATTATTTGACATTCCTAAAGAAAGGAAGAATGCAGAGTATAAGAGATACCTAGAGATGCTGCTTGAG
TAACTTCAGGATTACACAGATAGAGTAAAGCCTCTCCAAGATCAGAATGAACTTTTGGGGAAGATTCAGGCTGAGTTTGA
GAAGAAATGGGAGAATGTGACCTTCCTGGATGGGCGAAAGAGACAAGCAGCGCTCTGACCCATGCTGGAGCCCATCTTGA
CCTCTCCGCATTCTCCTCCTGGGAGGAGTTGGCCTCTCTGGGTTTGGACAGATTGAAATCTGCTCTCTTTGCTTTAGGCT
TGAAATGTGGCGGACTGTAGAAGAGCAAGCCCAGAGACTATTCAGCACCAAAGGAAAGTCCCTGGAGTCACTTGATAAGT
CTTTGTTTGCCAAAAATCCCAAATCAAAGGGCACCAAGCGAGACATTGAGAGAACAAAGACATTGCTTTTCTAGAAGCCC
AGATCTATGAATACTCTGACTCTCAGGGA

Alignment

ORF - retro_ptro_1411 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.68 %
• Parental protein coverage: 66.87 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  METILEQQRRYHEEKERLMDVMAKEMLTKKSTLRDQINSDHRTRAMQDRYMEVSGNLRDLYDDKDGLRKE
          METI.EQQRRYHEEK.RLMDVMAKEMLTKKST.....NSDHR..AMQDRYMEVSGNLRDLYDDKDGL.KE
Retrocopy METIPEQQRRYHEEKGRLMDVMAKEMLTKKST----LNSDHRAQAMQDRYMEVSGNLRDLYDDKDGL*KE

Parental  ELNAISGPNEFAEFYNRLKQIKEFHRKHPNEICVPMSVEFEELLKAR-ENPSEEAQNLVEFTDEEGYGRY
          ELNAISGPNEFAEFYNRL..IKEFH.KHPNEICVPMSVEFEELLKA...NPSEEAQNLVEFTDEEGYGRY
Retrocopy ELNAISGPNEFAEFYNRLE*IKEFHQKHPNEICVPMSVEFEELLKAQ<DNPSEEAQNLVEFTDEEGYGRY

Parental  LDLHDCYLKYINLKASEKLDYITYLSIFDQLFDIPKERKNAEYKRYLEMLLEYLQDYTDRVKPLQDQNEL
          LDL.DCYLKYIN.KASEKLDYITYLSI.DQLFDIPKERKNAEYKRYLEMLLE.LQDYTDRVKPLQDQNEL
Retrocopy LDLRDCYLKYINVKASEKLDYITYLSISDQLFDIPKERKNAEYKRYLEMLLE*LQDYTDRVKPLQDQNEL

Parental  FGKIQAEFEKKWENGTF-PGWPKETSSALTHAGAHLDLSAFSSWEELASLGLDRLKSALLALGLKCGG-T
          .GKIQAEFEKKWEN.TF.PGW.KETSSALTHAGAHLDLSAFSSWEELASLGLDRLKSAL.ALGLKCGG.T
Retrocopy LGKIQAEFEKKWENVTF<PGWAKETSSALTHAGAHLDLSAFSSWEELASLGLDRLKSALFALGLKCGG<T

Parental  LEERAQRLFSTKGKSLESLDTSLFAKNPKSKGTKRDTER-NKDIAFLEAQIYEYVEILG
          .EE.AQRLFSTKGKSLESLD.SLFAKNPKSKGTKRD.ER.NKDIAFLEAQIYEY....G
Retrocopy VEEQAQRLFSTKGKSLESLDKSLFAKNPKSKGTKRDIER<NKDIAFLEAQIYEYSDSQG

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	34.00 RPM
SRP007412_cerebellum	0.22 RPM	60.58 RPM
SRP007412_heart	0.12 RPM	33.23 RPM
SRP007412_kidney	0.05 RPM	49.79 RPM
SRP007412_liver	0.03 RPM	38.95 RPM
SRP007412_testis	0.11 RPM	142.48 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1411 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1411 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1411 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2441
Macaca mulatta	retro_mmul_631

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001262	1 retrocopy	retro_amel_485,
Canis familiaris	ENSCAFG00000003222	1 retrocopy	retro_cfam_176,
Callithrix jacchus	ENSCJAG00000002176	1 retrocopy	retro_cjac_4109,
Cavia porcellus	ENSCPOG00000008660	1 retrocopy	retro_cpor_658,
Homo sapiens	ENSG00000183431	2 retrocopies	retro_hsap_2441, retro_hsap_937,
Macropus eugenii	ENSMEUG00000002534	3 retrocopies	retro_meug_1135, retro_meug_1346, retro_meug_642,
Macaca mulatta	ENSMMUG00000023199	1 retrocopy	retro_mmul_631,
Monodelphis domestica	ENSMODG00000017729	1 retrocopy	retro_mdom_269,
Nomascus leucogenys	ENSNLEG00000011720	1 retrocopy	retro_nleu_2775,
Pan troglodytes	ENSPTRG00000000559	2 retrocopies	retro_ptro_1411 , retro_ptro_649,
Sorex araneus	ENSSARG00000014204	1 retrocopy	retro_sara_407,