RetrogeneDB ID: retro_ptro_1035

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 15:92283199..92284326(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GLTSCR2
• Ensembl ID: ENSPTRG00000011215
• Aliases: None
• Description: None

Sequence

>retro_ptro_1035
ATGGCGGCAGGAGGCAGTGGCGTTGGTGGGAAGCACAGCTCGAAAAGCGATAACGATTCTGGTTTCCTGGGGCTGCGGCC
CATTTCGGCGGACCCAGCGCTGAGGCGGCGGCGGCGAGGCCCAGGAAATAAGAAGTGGGGCTGGCGGCGGCTTGCTCAGG
AGCCGCTGGGGCTGGAGGTTGACCAGTTCCTGGAAGACGTGCGGCTACAGGAGCGCATGAGCGGTGGCTTGTTGAGAGAG
GCCCCAAATGAAACACTCTTCTTCCTGGACACCGGCTCCAAGGAAAAAGGGCTAAGAAGAGAACCAAAGTCCAGAAGAAG
TCACTGCTTCTCAAGAAACCCCTTCGGGTTGACCTCATCCTCGAGACACATCCAAAGTCCCTGCCCCCAAAGACGTCCTC
GCCCACCAGGTCCCGAACGCCAAGAAGCTCAGGCGGAAGGAGCAGCTATGGGAGAATCTGGCCAAGCAGGGCGAGCTGCC
CCGGGAGGTGCGCAGGGCCCAGGCCCGGCTCCTCAACCCTCCCACAGCCGGGCCCCAGGACACCGTGGAGCGGCCCTTCC
ACGACCTCTGGGCCTCAGACAACCCCCTGGACAGGCCATCGTTTGGCCAGGATGAGTTTTTCCTGGAGCAGACCAAGAAG
AAAGGAGTGAAGCGGCCACCACGCCTGCACACCAAGCCGTCCCAGACACCCGCCGTGGAGGTGGCGCCTGCCGGAGCTTC
CTACGACCCGTACTTTGAAGACCACCGGACCCTGCTCTCAGCGGCCCACGAGGTGGAGTTGCAGCGGCAGAAGGAGGCGG
AGAAGCCGGAGCGGCAGCTGGCCCTGCCCGCCACAGAGCAGGCCGCCACCCAGGAGTCCACGTTCCAGGTAGCCGTGCGA
GGGGCTGCTGGAGGAGTCGGAGGGTTCGGGGGAGCCGGGCCAGGGCGAGGGGCCGGAGGCTGGGGATGCCGAGGTCTGTC
CCACGCCCGCCCGCCCGGCCGCCACAGAGAAGGAGACGGAGCAGCGGCGGCGGCGGGAGAAGGCTGCGCGCAGGCTGCGG
GTACAGCAGGCCGCGTTGCGGACTGCCAGGCTCCGGCACTGGCACCAGGAGGTGTTCCTGCTGCGCGGGATCAAGGCCCA
GGTGGCC

Alignment

ORF - retro_ptro_1035 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.68 %
• Parental protein coverage: 79.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAAGGSGVGGKRSSKSDADSGFLGLRPTSVDPALRRRRRGPRNKKRGWRRLAQEPLGLEVDQFLEDVRLQ
          MAAGGSGVGGK.SSKSD.DSGFLGLRP.S.DPALRRRRRGP.NKK.GWRRLAQEPLGLEVDQFLEDVRLQ
Retrocopy MAAGGSGVGGKHSSKSDNDSGFLGLRPISADPALRRRRRGPGNKKWGWRRLAQEPLGLEVDQFLEDVRLQ

Parental  ERTSGGLLSEAPNEKLFFVDTGSKEKGL-TKKRTKVQKKSLLLKKPLRVDLILE-NTSKVPAPKDVLAHQ
          ER.SGGLL.EAPNE.LFF.DTGSKEKGL..K......K..LL.KKPLRVDLILE..TSKVPAPKDVLAHQ
Retrocopy ERMSGGLLREAPNETLFFLDTGSKEKGL<KKRTKVQKKSLLL-KKPLRVDLILE<DTSKVPAPKDVLAHQ

Parental  VPNAKKLRRKEQLWEKLAKQGELPREVRRAQARLLNPSAARAKPGPQDTVERPFYDLWASDNPLDRPLVG
          VPNAKKLRRKEQLWE.LAKQGELPREVRRAQARLLNP..A....GPQDTVERPF.DLWASDNPLDRP..G
Retrocopy VPNAKKLRRKEQLWENLAKQGELPREVRRAQARLLNPPTA----GPQDTVERPFHDLWASDNPLDRPSFG

Parental  QDEFFLEQTKKKGVKRPARLHTKPSQAPAVEVAPAGASYNPSFEDHQTLLSAAHEVELQRQKEAEKLERQ
          QDEFFLEQTKKKGVKRP.RLHTKPSQ.PAVEVAPAGASY.P.FEDH.TLLSAAHEVELQRQKEAEK.ERQ
Retrocopy QDEFFLEQTKKKGVKRPPRLHTKPSQTPAVEVAPAGASYDPYFEDHRTLLSAAHEVELQRQKEAEKPERQ

Parental  LALPTTEQAATQESTFQEL-CEGLLEESDGEGEPGQGEGPEAGDAEVCPTPARLATTEKKTEQQRRREKA
          LALP.TEQAATQESTFQ...CEGLLEES.G.GEPGQGEGPEAGDAEVCPTPAR.A.TEK.TEQ.RRREKA
Retrocopy LALPATEQAATQESTFQVA>CEGLLEESEGSGEPGQGEGPEAGDAEVCPTPARPAATEKETEQRRRREKA

Parental  AHRLRVQQAALRAARLR--HQELFRLRGIKAQVA
          A.RLRVQQAALR.ARLR..HQE.F.LRGIKAQVA
Retrocopy ARRLRVQQAALRTARLRHWHQEVFLLRGIKAQVA

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	55.20 RPM
SRP007412_cerebellum	0.11 RPM	101.70 RPM
SRP007412_heart	0.00 RPM	42.61 RPM
SRP007412_kidney	0.03 RPM	138.68 RPM
SRP007412_liver	0.07 RPM	141.87 RPM
SRP007412_testis	2.63 RPM	35.62 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1035 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1035 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1035 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1528
Pongo abelii	retro_pabe_1270

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000105373	1 retrocopy	retro_hsap_1528,
Macropus eugenii	ENSMEUG00000002525	2 retrocopies	retro_meug_1136, retro_meug_1713,
Nomascus leucogenys	ENSNLEG00000003143	1 retrocopy	retro_nleu_1937,
Pongo abelii	ENSPPYG00000010181	3 retrocopies	retro_pabe_1270, retro_pabe_653, retro_pabe_662,
Pan troglodytes	ENSPTRG00000011215	1 retrocopy	retro_ptro_1035 ,
Rattus norvegicus	ENSRNOG00000013023	1 retrocopy	retro_rnor_1107,