RetrogeneDB ID: retro_ptro_3143

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:90131872..90132974(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: USP12
• Ensembl ID: ENSPTRG00000005727
• Aliases: USP12, USP12P1
• Description: Ubiquitin carboxyl-terminal hydrolase [Source:UniProtKB/TrEMBL;Acc:H2Q7B8]

Sequence

>retro_ptro_3143
ATGGAAATCCTAATGACAGTCTCCAAATTCGCCTCCATCTGTACCATGGGCGCCAGTGCTTCGGCATTAGAGAAAGAGAT
TGGTCCAGAACAGTTTCCGGTCAACGAGCATTATTTTGGATTAGTCAATTTTGGGAATACCTGCTACTGCAATTCAGTTC
TTCAAGCACTTTATTTTTGTCGTCCGTTTCGGGAAAAAGTTCTTGCATATAAGAGTCAACCTAGGAAAAAGGAGAGCCTT
CTTACATGCTTAGCAGATCTCTTTCACAGCATAGCCACTCAGAAGAAAAAGGTTGGAGGAATACCTCCGAAGAAGTTCGG
ATTACAGAAAGAAAATGAGCTTTTCGACAACTACATGCAACAAGATGCCCATGAATTCTTAAATTACCTACTAAATACAA
CTGGTGATATTTTACAAGAAGAGAGAAAGCAGGAAAAACAAAATGGTCGCTAACCTAATGATAATATTGATAATGAAAAT
AATAGCAGCACACCAGACCCAACGTGGGTTCATGAGATTTTTCGGGGAACGTTAACTAATGAAACAGACGTCTTACTTGT
GAAACTATAAGCAGCAAAGATGAAGATTTTTTAGACCTTTCTGTTGACGTGGAACAAAATACATCAATTACTCACTGCTT
AAGGGGTTTCAGCAACACAGAAACTCTATGCAGTTAATACAAGTATTACTGTGAAGAGTGTCGCAGCAAACAGGAAGCAC
ACAAACAGATGAAAGTTTAAAAACTGCCCATGATTCTAGCTCTACACTTGAAGAGATTTAAATATATGGATCAACTTCAT
CGATATACAAAACTCTCTTACCGGGTGGTTTTTCCTTTAGAACTTCGTCTATTTAACACTTCAGGTGATGCCACCAATCC
AGACAGAATGTACGACCTTGTTGCTGTTGTGGTTCACTGTGGAAGTGGTCCCAATCGAGGCCATTATATTGCGATAGTTA
AGAGTCATGATTTTTGGTTGTTGTTTGATGACGACATTGTAGAAAAAATAGATACACAAGCTATTGAAGAATTCTACGGG
TTGACATCAGATACTCAAAGAACTCTGAGTCTGGTTACATCCTTTTCTATCAGTCTCGGGAC

Alignment

ORF - retro_ptro_3143 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.62 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MEILMTVSKFASICTMGANASALEKEIGPEQFPVNEHYFGLVNFGNTCYCNSVLQALYFCRPFREKVLAY
          MEILMTVSKFASICTMGA.ASALEKEIGPEQFPVNEHYFGLVNFGNTCYCNSVLQALYFCRPFREKVLAY
Retrocopy MEILMTVSKFASICTMGASASALEKEIGPEQFPVNEHYFGLVNFGNTCYCNSVLQALYFCRPFREKVLAY

Parental  KSQPRKKESLLTCLADLFHSIATQKKKVGVIPPKKFITRLRKENELFDNYMQQDAHEFLNYLLNTIADIL
          KSQPRKKESLLTCLADLFHSIATQKKKVG.IPPKKF...L.KENELFDNYMQQDAHEFLNYLLNT..DIL
Retrocopy KSQPRKKESLLTCLADLFHSIATQKKKVGGIPPKKF--GLQKENELFDNYMQQDAHEFLNYLLNTTGDIL

Parental  QEERKQEKQNGRLPNGNIDNENNNSTPDPTWVHEIFQGTLTNET-RCLTCETISSKDEDFLDLSVDVEQN
          QEERKQEKQNGR.PN.NIDNENN.STPDPTWVHEIF.GTLTNET.R.LTCETISSKDEDFLDLSVDVEQN
Retrocopy QEERKQEKQNGR*PNDNIDNENNSSTPDPTWVHEIFRGTLTNET<RRLTCETISSKDEDFLDLSVDVEQN

Parental  TSITHCLRGFSNTETLCSEYKYYCEECRSKQEAHKRMKVKKLPMILALHLKRFKYMDQLHRYTKLSYRVV
          TSITHCLRGFSNTETLCS.YKYYCEECRSKQEAHK.MKV.KLPMILALHLKRFKYMDQLHRYTKLSYRVV
Retrocopy TSITHCLRGFSNTETLCS*YKYYCEECRSKQEAHKQMKV*KLPMILALHLKRFKYMDQLHRYTKLSYRVV

Parental  FPLELRLFNTSGDATNPDRMYDLVAVVVHCGSGPNRGHYIAIVKSHDFWLLFDDDIVEKIDAQAIEEFYG
          FPLELRLFNTSGDATNPDRMYDLVAVVVHCGSGPNRGHYIAIVKSHDFWLLFDDDIVEKID.QAIEEFYG
Retrocopy FPLELRLFNTSGDATNPDRMYDLVAVVVHCGSGPNRGHYIAIVKSHDFWLLFDDDIVEKIDTQAIEEFYG

Parental  LTSD-ISKNSESGYILFYQSRD
          LTSD..SKNSESGYILFYQSRD
Retrocopy LTSD<YSKNSESGYILFYQSRD

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	42.08 RPM
SRP007412_cerebellum	0.00 RPM	43.88 RPM
SRP007412_heart	0.06 RPM	34.10 RPM
SRP007412_kidney	0.05 RPM	42.03 RPM
SRP007412_liver	0.13 RPM	32.83 RPM
SRP007412_testis	0.00 RPM	40.47 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3143 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3143 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3143 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4726
Homo sapiens	retro_hsap_4918
Gorilla gorilla	retro_ggor_2937
Pongo abelii	retro_pabe_3672

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019344	5 retrocopies	retro_cjac_2734, retro_cjac_3901, retro_cjac_3964, retro_cjac_3965, retro_cjac_4011,
Homo sapiens	ENSG00000152484	4 retrocopies	retro_hsap_2328, retro_hsap_3266, retro_hsap_4726, retro_hsap_4918,
Microcebus murinus	ENSMICG00000006269	2 retrocopies	retro_mmur_1167, retro_mmur_1187,
Macaca mulatta	ENSMMUG00000021425	1 retrocopy	retro_mmul_937,
Nomascus leucogenys	ENSNLEG00000000323	3 retrocopies	retro_nleu_1817, retro_nleu_1995, retro_nleu_2426,
Otolemur garnettii	ENSOGAG00000030639	1 retrocopy	retro_ogar_2897,
Pongo abelii	ENSPPYG00000005232	3 retrocopies	retro_pabe_2110, retro_pabe_2705, retro_pabe_3672,
Pan troglodytes	ENSPTRG00000005727	3 retrocopies	retro_ptro_1701, retro_ptro_2209, retro_ptro_3143 ,
Tupaia belangeri	ENSTBEG00000012960	2 retrocopies	retro_tbel_3285, retro_tbel_4692,