RetrogeneDB ID: retro_ptro_1985

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:51862715..51863414(+)
• Located in intron of: ENSPTRG00000016200

Retrocopy information

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

Parental gene information

• Parental gene symbol: SERBP1
• Ensembl ID: ENSPTRG00000023560
• Aliases: None
• Description: SERPINE1 mRNA binding protein 1 [Source:HGNC Symbol;Acc:17860]

Sequence

>retro_ptro_1985
ATGCCTGGGCACTTACAGGAAGGCTTCGGCTGTGTGGTCACCAACCGATTCGACCAGTTATTTGACGACGAATCGGACCC
CTTCGAGGTGCTGAAGGCAGCGGAGAACAAGAAAAAAGAAGCCGGCAGGGGTGGCGTTGGGGGCCCTGGGGCCAAGAGCG
CAGCTCAGGCGGCGGCCCAGACCAACTCCAACGCGGCAGGCAAACAGCTGCGCAAGGAGTCCCAGAAAGACCGCAAGAAC
CCGCTGCCCCCTAGCGTTGGCGTGGTTGACAAGAAAGAGGAGACGCAGCCGCCCGTGGCGCCTAAGAAAGAAGGAATAAG
ACGAGTTGGAAGAAGACCTGATCAACAACTTCAGGGTGAAGGGAAAATAATTGATAGAAGACCAGAAAGGCAACCACCTT
GTGAACGAAGATTCGAAAAGCCACTTGAAGAAAAGGGTGAAGGAGGCGAATTTTCAGTTGATAGACCGATTATTGACCGA
CCTATTCGAGGTCGTGGTGGTCTTGGAAGAGGTCGAGGGGGCCGTGGACGTGGAATGGGCCGAGGAGATGGATTTGATTC
TCGTGGCAAACGTGAATTTGATAGGCATAGTGGAAGTGATAGATCTTCTTTTTCACATTACAGTGGCCTGAAGCACGAGG
ACAAACGTGGAGGTAGCGGATCTCACAACTGGGGAACTGTCAAAGACGAATTAACTGAC

Alignment

ORF - retro_ptro_1985 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.85 %
• Parental protein coverage: 57.11 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPGHLQEGFGCVVTNRFDQLFDDESDPFEVLKAAENKKKEAGGGGVGGPGAKSAAQAAAQTNSNAAGKQL
          MPGHLQEGFGCVVTNRFDQLFDDESDPFEVLKAAENKKKEAG.GGVGGPGAKSAAQAAAQTNSNAAGKQL
Retrocopy MPGHLQEGFGCVVTNRFDQLFDDESDPFEVLKAAENKKKEAGRGGVGGPGAKSAAQAAAQTNSNAAGKQL

Parental  RKESQKDRKNPLPPSVGVVDKKEETQPPVALKKEGIRRVGRRPDQQLQGEGKIIDRRPERRPPRERRFEK
          RKESQKDRKNPLPPSVGVVDKKEETQPPVA.KKEGIRRVGRRPDQQLQGEGKIIDRRPER.PP.ERRFEK
Retrocopy RKESQKDRKNPLPPSVGVVDKKEETQPPVAPKKEGIRRVGRRPDQQLQGEGKIIDRRPERQPPCERRFEK

Parental  PLEEKGEGGEFSVDRPIIDRPIRGRGGLGRGRGGRGRGMGRGDGFDSRGKREFDRHSGSDRSSFSHYSGL
          PLEEKGEGGEFSVDRPIIDRPI..............RGMGRGDGFDSRGKREFDRHSGSDRSSFSHYSGL
Retrocopy PLEEKGEGGEFSVDRPIIDRPIXXXXXXXXXXXXXXRGMGRGDGFDSRGKREFDRHSGSDRSSFSHYSGL

Parental  KHEDKRGGSGSHNWGTVKDELTE
          KHEDKRGGSGSHNWGTVKDELT.
Retrocopy KHEDKRGGSGSHNWGTVKDELTD

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	2.95 RPM	54.14 RPM
SRP007412_cerebellum	6.20 RPM	64.53 RPM
SRP007412_heart	5.74 RPM	64.76 RPM
SRP007412_kidney	6.28 RPM	76.83 RPM
SRP007412_liver	11.46 RPM	84.06 RPM
SRP007412_testis	29.51 RPM	128.67 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1985 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1985 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1985 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3056

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018538	1 retrocopy	retro_cfam_546,
Callithrix jacchus	ENSCJAG00000017440	2 retrocopies	retro_cjac_1207, retro_cjac_3015,
Homo sapiens	ENSG00000142864	3 retrocopies	retro_hsap_3056, retro_hsap_413, retro_hsap_4695,
Gorilla gorilla	ENSGGOG00000010396	1 retrocopy	retro_ggor_408,
Myotis lucifugus	ENSMLUG00000001424	1 retrocopy	retro_mluc_691,
Otolemur garnettii	ENSOGAG00000025884	1 retrocopy	retro_ogar_185,
Pan troglodytes	ENSPTRG00000023560	2 retrocopies	retro_ptro_1985 , retro_ptro_317,
Tupaia belangeri	ENSTBEG00000003689	4 retrocopies	retro_tbel_1004, retro_tbel_1331, retro_tbel_2427, retro_tbel_532,