RetrogeneDB ID: retro_ptro_2281

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:89405032..89406431(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000021972
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RDX
• Ensembl ID: ENSPTRG00000004259
• Aliases: None
• Description: Radixin [Source:UniProtKB/TrEMBL;Acc:K7DB88]

Sequence

>retro_ptro_2281
ATGCCCAAAACGATCAGTGTGCGTGTGACCACCATGGATGCAGAGCTGGAGTTTACCATCCAGCCCAACACCACCGGGAA
GCAGCTATTTGACCAGGTGGTGAAAACTGTTGGCTTGAGGGAAGTTTGTTTCTTTGGTCTGCAGTACCAGGACACCAAAG
GTTTCTCCACCTGGCTGAAACTCAATTAAGAAGGTGACTGCCCAGGAAGTGCGGAAGGAAAGCCCCCTGCTCTTTAAGTT
CAGTGCCAAGTTCTACCCTGAGGATGTGTCCGAGGAATTGATTCAGGACACCATTCAGCGTCTGTTCTTTCTGCAAGTGA
AAGAGGGCATTCTCAATGATGATATTTACTGCTGGCCTGAGACTGCTGTGCTGCTGGCCTCCCATGCTGTCCAGTCTAAG
TATGGGAACTTCAGTAAGGAGGTGCATAAGTCTGGCTACCTGGCCGGAGACGAGTTGCTCCCACAGAGAGTCCTGGAAAA
GCACAAACTCAGCAAGGACCAGTGGGAGGAGCGGATCCAGGTGTGGCATGAGGAACACCGTGGCATGCTCAGGGAGGATG
CTGTCCTGGAATATCTGAAGATTGCTCAAGATCTGGAGATGTATGGTGTAAACTACTTCAGCATCAAGAAAAAGAAAGGC
TCAGAGCTGTGGCTGGGGGTGGATGCACTGGGTCTCAACATCTATGAGCAGCATGACAGACTAACTCCCAAGATAGGCTT
TCCTTGGAGTGAAATCAGGAGCATTTCTTTCAATGATAAGAAATTTGTCATCAAGCCCATTGACAAAAAAGCCCCGGACT
TTGTCTTCTATGCTCCCTGGCTGCGGATTAACAAGCGGATCTTGGCCTTGTGCATGGGGAACCATGAACTATACATGCGC
AGTCGCAAGCCTGACACCATTGAGGTGCAGCAGATGAAGGCACAGGCCCGGGAGGAGAAGCACCAGAAGCAGATGGAGCG
TGCTATGCTGGAAAATGAGAAGAAGCGTGAAATGGCAGAAAAGGAGAAAGAGAAGATTGAACGGGAGAAGGAGCTGATGG
AGAGGCTGAAGCAGATCGAGGAACAGACTAAGAAGGCTCAGCAAGAACTGGAAGAACAGACCCGTAGGGCTCTGGAACTT
GGGAAGGAACGGAAGCATGCCCAGAGTGAGGCTGAAAAGCTGGCCAAGGAGCTTCAAGAAGCTGAAGAGGCCAAGGAAGT
CTTGCTGCAGGCCTCCCGGGACCAGAAAAAGACTCAGGAATAGCTGGCCTTGGAAATGGCAGAGCTGACAGCTCAAATCT
CTCAGCTGGAACTGGCCTGACAGAAGAAAGAGAGTGAGGCTATGGAGTCGCAGCAGAAGGCCCAGATGGTACAGGAAGAC
TTGGAGAAGACCCGTGCTGAGCTGAAGACTGCCATGAGT

Alignment

ORF - retro_ptro_2281 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.74 %
• Parental protein coverage: 77.48 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPKPINVRVTTMDAELEFAIQPNTTGKQLFDQVVKTVGLREVWFFGLQYVDSKGYSTWLKLN-KKVTQQD
          MPK.I.VRVTTMDAELEF.IQPNTTGKQLFDQVVKTVGLREV.FFGLQY.D.KG.STWLKLN.KKVT.Q.
Retrocopy MPKTISVRVTTMDAELEFTIQPNTTGKQLFDQVVKTVGLREVCFFGLQYQDTKGFSTWLKLN>KKVTAQE

Parental  VKKENPLQFKFRAKFFPEDVSEELIQEITQRLFFLQVKEAILNDEIYCPPETAVLLASYAVQAKYGDYNK
          V.KE.PL.FKF.AKF.PEDVSEELIQ...QRLFFLQVKE.ILND.IYC.PETAVLLAS.AVQ.KYG...K
Retrocopy VRKESPLLFKFSAKFYPEDVSEELIQDTIQRLFFLQVKEGILNDDIYCWPETAVLLASHAVQSKYGNFSK

Parental  EIHKPGYLANDRLLPQRVLEQHKLTKEQWEERIQNWHEEHRGMLREDSMMEYLKIAQDLEMYGVNYFEIK
          E.HK.GYLA.D.LLPQRVLE.HKL.K.QWEERIQ.WHEEHRGMLRED...EYLKIAQDLEMYGVNYF.IK
Retrocopy EVHKSGYLAGDELLPQRVLEKHKLSKDQWEERIQVWHEEHRGMLREDAVLEYLKIAQDLEMYGVNYFSIK

Parental  NKKGTELWLGVDALGLNIYEHDDKLTPKIGFPWSEIRNISFNDKKFVIKPIDKKAPDFVFYAPRLRINKR
          .KKG.ELWLGVDALGLNIYE..D.LTPKIGFPWSEIR.ISFNDKKFVIKPIDKKAPDFVFYAP.LRINKR
Retrocopy KKKGSELWLGVDALGLNIYEQHDRLTPKIGFPWSEIRSISFNDKKFVIKPIDKKAPDFVFYAPWLRINKR

Parental  ILALCMGNHELYMRRRKPDTIEVQQMKAQAREEKHQKQLERAQLENEKKKREIAEKEKERIEREKEELME
          ILALCMGNHELYMR.RKPDTIEVQQMKAQAREEKHQKQ.ERA.LENE.KKRE.AEKEKE.IEREK.ELME
Retrocopy ILALCMGNHELYMRSRKPDTIEVQQMKAQAREEKHQKQMERAMLENE-KKREMAEKEKEKIEREK-ELME

Parental  RLKQIEEQTIKAQKELEEQTRKALELDQERKRAKEEAERLEKERRAAEEAKSAIAKQAADQMKNQEQLAA
          RLKQIEEQT.KAQ.ELEEQTR.ALEL..ERK.A..EAE.L.KE...AEEAK........DQ.K.QE.LA.
Retrocopy RLKQIEEQTKKAQQELEEQTRRALELGKERKHAQSEAEKLAKELQEAEEAKEVLLQASRDQKKTQE*LAL

Parental  ELAEFTAKIALLEEAKKKKEEEATEWQHKAFAAQEDLEKTKEELKTVMS
          E.AE.TA.I..LE.A..KKE.EA.E.Q.KA...QEDLEKT..ELKT.MS
Retrocopy EMAELTAQISQLELA*QKKESEAMESQQKAQMVQEDLEKTRAELKTAMS

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	4.90 RPM	19.39 RPM
SRP007412_cerebellum	10.54 RPM	22.98 RPM
SRP007412_heart	24.60 RPM	31.83 RPM
SRP007412_kidney	35.49 RPM	37.79 RPM
SRP007412_liver	24.68 RPM	24.88 RPM
SRP007412_testis	1.69 RPM	34.46 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2281 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2281 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2281 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3153
Gorilla gorilla	retro_ggor_1359
Pongo abelii	retro_pabe_2623

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000019413	1 retrocopy	retro_dnov_1663,
Homo sapiens	ENSG00000137710	1 retrocopy	retro_hsap_840,
Gorilla gorilla	ENSGGOG00000027218	1 retrocopy	retro_ggor_689,
Pan troglodytes	ENSPTRG00000004259	1 retrocopy	retro_ptro_2281 ,