RetrogeneDB ID: retro_ptro_1934

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:152629473..152631251(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000040698
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: UBQLN4
• Ensembl ID: ENSPTRG00000001444
• Aliases: None
• Description: None

Sequence

>retro_ptro_1934
ACGAGGCCCCCCATTCGGGTCACCGTCAAGACCCCCAAGGACAAGGAGGAAATTGTGATCTGCGATCGAGCCTCGGTCAA
GGAGTTCAAAGAGGAAATCTCCCGGAGGTTTAAGGCTCAGCAGGATCAGCTGGTCCTGATCTTCGCAGGCAAGATCCTCA
AGGATGGGGACACACTGAACCAGCACGGAATCAAGGACGGGCTCACTGTCCATCTGGTCATCAAGACCCCTCAGAAGGCT
CAAGATCCAGCTGCTGCCACTGCTTCTTCCCCCTCCACACCTGACCCTGCCTCAGCACCCTCCACCACGCCTGCTTCACC
CGCCACCCCTACCCAGCCCTCCACCTCTGACAGTGCCTCTTCGGATGCTGGCAGTGGAAGCCGGAGGAGCAGTGGTGGGG
GGCCCTCTCCAGGGGCTGGGGAGGGATCCCCCAGTGCTACTGCGTCCATACTCTCTGGCTTTGGGGGCATCCTGGGGCTG
GGCAGCCTGGGCCTGGGCTCTGCCAACTTCATGGAGCTGCAGCAGCAGATGCAGAGGCAGCTGATGTCCAATCCTGAGAT
GCTGTCGCAGATCATGGAGAACCCCCTGGTCCAGGATATGATGTCTAACCCTGACCTGATGCGTCACATGATTATTGCCA
ACCCCCAGATGCAGCAGTTGATGGAGCGGAACCCTGAGATCAGCCACATGCTCAATAACCCTGAACTCATGAGGCAGACA
ATGGAGCTTGCTCGGAATCCAGCCATGATGCAAGAGATGATGCGGAACCAGGACCGGGCCCTGAGCAACCTTGAGAGCAT
CCCTGGAGGGTATAATGCCCTCCGCCACATGTACACGGACATCCAGGAGCCCATGTTCAGTGCTGCCCGGGAACAGTTTG
GCAACAGTCCCTTCTCTTCCCTGGCCGGGAACTCCGACAGCTCATCCTCCCAGCCTCTGCGGACTGAGAATCGAGAGCCC
CTCCCTAACCCCTGGAGCCCCTCGCCCCCCACCTCCCAGGCCCCCGGGTCCGGTGGGGAGGGCACCGGAGGATCGGGGAC
CAGCCAGGTGCACCCGACAGTCTCGAACCCCTTTGGGATCAATGCGGCTAGCCTGAGGTCAGGGATGTTCAATAGCCCAG
AAATGCAAGCCTCCTCCAGCAGATCTCTGAGAACCCCCAGCTGATGCAGAATGTGATCTCAGCACCCTACATGCGCAGCA
TGATGCAGACGCTTGCCCAGAACCCCAACTTCGCTGCTCAGATGATGGTGAATGTGCCGCTCTTCGCGGGGAACCCCCAA
CTGCAGGAGCAGCTCCGCCTGCAGCTCCCAGTCTTCCTGCAGCAGATGCAGAACCCAGAGTCACTCTCTATCCTCACCAA
TCCCCGAGCCATTCAGGCATTGCTGCAGATCCAGCAGGGACTACAGACCTTGCAGACCGAGGCCCCTGGGCTGGTACCCA
GCCTTGTCTCCTTTGGGATGTCCCGGACCCCAGCACCCTCAGCAGGCAGCAACGCAGGGTCTACGCCCGAGGCCCCCACT
TCCTCACCAGCCACGCCAGCCACATCTTCTCCAACAGGGGCTTCCAGCACCCAGCAGCAACTCATGCAGCAGATGATCCA
GCTTTTGGCTGGAAGTGGAAACTCACAGGTGCAGACGCCAGAAGTGAGATTTCAGCAGCAGCTGGAGCAGCTCAACTCCA
TGGGCTTCATCAATCGTGAGGCCAACCTGCAGGCCCTGATTGCCACAGGAGGGGACATCAACGCAGCTATCGAGAGACTG
CTGGGCTCCCAGCTCTCC

Alignment

ORF - retro_ptro_1934 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.6 %
• Parental protein coverage: 98.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TRPPIRVTVKTPKDKEEIVICDRASVKEFKEEISRRFKAQQDQLVLIFAGKILKDGDTLNQHGIKDGLTV
          TRPPIRVTVKTPKDKEEIVICDRASVKEFKEEISRRFKAQQDQLVLIFAGKILKDGDTLNQHGIKDGLTV
Retrocopy TRPPIRVTVKTPKDKEEIVICDRASVKEFKEEISRRFKAQQDQLVLIFAGKILKDGDTLNQHGIKDGLTV

Parental  HLVIKTPQKAQDPAAATASSPSTPDPASAPSTTPASPATPAQPSTSGSASSDAGSGSRRSSGGGPSPGAG
          HLVIKTPQKAQDPAAATASSPSTPDPASAPSTTPASPATP.QPSTS.SASSDAGSGSRRSSGGGPSPGAG
Retrocopy HLVIKTPQKAQDPAAATASSPSTPDPASAPSTTPASPATPTQPSTSDSASSDAGSGSRRSSGGGPSPGAG

Parental  EGSPSATASILSGFGGILGLGSLGLGSANFMELQQQMQRQLMSNPEMLSQIMENPLVQDMMSNPDLMRHM
          EGSPSATASILSGF............SANFMELQQQMQRQLMSNPEMLSQIMENPLVQDMMSNPDLMRHM
Retrocopy EGSPSATASILSGFXXXXXXXXXXXXSANFMELQQQMQRQLMSNPEMLSQIMENPLVQDMMSNPDLMRHM

Parental  IMANPQMQQLMERNPEISHMLNNPELMRQTMELARNPAMMQEMMRNQDRALSNLESIPGGYNALRRMYTD
          I.ANPQMQQLMERNPEISHMLNNPELMRQTMELARNPAMMQEMMRNQDRALSNLESIPGGYNALR.MYTD
Retrocopy IIANPQMQQLMERNPEISHMLNNPELMRQTMELARNPAMMQEMMRNQDRALSNLESIPGGYNALRHMYTD

Parental  IQEPMFSAAREQFGNNPFSSLAGNSDSSSSQPLRTENREPLPNPWSPSPPTSQAPGSGGEGTGGSGTSQV
          IQEPMFSAAREQFGN.PFSSLAGNSDSSSSQPLRTENREP...............GSGGEGTGGSGTSQV
Retrocopy IQEPMFSAAREQFGNSPFSSLAGNSDSSSSQPLRTENREPXXXXXXXXXXXXXXXGSGGEGTGGSGTSQV

Parental  HPTVSNPFGINAASLGSGMFNSPEMQA-LLQQISENPQLMQNVISAPYMRSMMQTLAQNPDFAAQMMVNV
          HPTVSNPFGINAASL.SGMFNSPEMQA.LLQQISENPQLMQNVISAPYMRSMMQTLAQNP.FAAQMMVNV
Retrocopy HPTVSNPFGINAASLRSGMFNSPEMQA<LLQQISENPQLMQNVISAPYMRSMMQTLAQNPNFAAQMMVNV

Parental  PLFAGNPQLQEQLRLQLPVFLQQMQNPESLSILTNPRAMQALLQIQQGLQTLQTEAPGLVPSLGSFGMSR
          PLFAGNPQLQEQLRLQLPVFLQQMQNPESLSILTNPRA.QALLQIQQGLQTLQTEAPGLVPSL.SFGMSR
Retrocopy PLFAGNPQLQEQLRLQLPVFLQQMQNPESLSILTNPRAIQALLQIQQGLQTLQTEAPGLVPSLVSFGMSR

Parental  TPAPSAGSNAGSTPEAPTSSPATPATSSPTGASSAQQQLMQQMIQLLAGSGNSQVQTPEVRFQQQLEQLN
          TPAPSAGSNAGSTPEAPTSSPATPATSSPTGASS.QQQLMQQMIQLLAGSGNSQVQTPEVRFQQQLEQLN
Retrocopy TPAPSAGSNAGSTPEAPTSSPATPATSSPTGASSTQQQLMQQMIQLLAGSGNSQVQTPEVRFQQQLEQLN

Parental  SMGFINREANLQALIATGGDINAAIERLLGSQLS
          SMGFINREANLQALIATGGDINAAIERLLGSQLS
Retrocopy SMGFINREANLQALIATGGDINAAIERLLGSQLS

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	0.38 RPM	65.69 RPM
SRP007412_cerebellum	0.14 RPM	49.54 RPM
SRP007412_heart	0.15 RPM	18.30 RPM
SRP007412_kidney	0.05 RPM	27.04 RPM
SRP007412_liver	0.26 RPM	24.62 RPM
SRP007412_testis	0.11 RPM	17.28 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1934 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1934 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1934 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2859
Gorilla gorilla	retro_ggor_26

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000160803	1 retrocopy	retro_hsap_2859,
Gorilla gorilla	ENSGGOG00000008916	1 retrocopy	retro_ggor_26,
Macropus eugenii	ENSMEUG00000016573	1 retrocopy	retro_meug_109,
Microcebus murinus	ENSMICG00000002222	1 retrocopy	retro_mmur_1146,
Macaca mulatta	ENSMMUG00000009983	1 retrocopy	retro_mmul_905,
Monodelphis domestica	ENSMODG00000016961	1 retrocopy	retro_mdom_530,
Pan troglodytes	ENSPTRG00000001444	1 retrocopy	retro_ptro_1934 ,
Pan troglodytes	ENSPTRG00000021055	1 retrocopy	retro_ptro_93,