RetrogeneDB ID: retro_pabe_2623

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:26702981..26704708(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MSN
• Ensembl ID: ENSPPYG00000020419
• Aliases: None
• Description: moesin [Source:HGNC Symbol;Acc:7373]

Sequence

>retro_pabe_2623
ATGCCCAAAACCACCAGTGTGGGCGTGACCACCATGGATGCAGAGCTGGAGTTTGCCATCCAGCCCAACACCACCGGGAA
GCAGCTATTTGACCAGGTGGTTAAAACTATTGGCTTGAGGGAAGTTTGGTTCTTTGGTCTGCAGTACCAGGACACTAAAG
GTTTCTCCACCTGGCTGAAACTCAATAAGAAGGTGACTGCCCAGGACGTGCGGAAGGAAAGCCCCCTGCTCTTTAAGTTC
AGTGCCAAGTTCTACCCTGAGGATGTGTCCGAGGAATTGATTCAGGACATCACTCAGCGTCTGTTCTTTCTGCAAGTGAA
ACAGGGCATTCTCAATGATGATATTTACTGCCCGCCTGAGACTGCTGTGCTGCTGGCCTCCTATGCTGTCCTGTCTAAGT
ATGGCAACTTCAATAAGGAGGTGCATAAGTCTGGCTACCTGGCCGGAGACAAGTTGCTCCCACAGAGAGTCCTGGAACAG
CACAAACTCAACAAGGACCAGTGGGAGGAGCGGATCCAGGTGTGGCATGAGGAACACGGTGGCATGCTCGGGGAGGATGC
TGTCCTGGAATATTGAAGATTACTCAAAATCTAGAGATGTATGGTGTGAACTACTTCAGCATCAAGAACAAGACAGGCTC
AGAGCTGTGGCTGGGGGTGGATGCTCTGGGTCTTAACATCTATGAGCAGAATGACAGACTAACTCCCAATATAGGCTTCC
CTTGGAGTGAAATCAGGAGCATTTCCTTCAATGATAAGAAATTTGTTATCAAGCCCATTGACAAAAAAGCCCCGGACTTA
GTCTTCTATGTTCCCTGGCTGCGGATTAACAAGTGGATCTTGGCCTTGTGCATGGGGAACCATGAACTATACATGCGCCG
TTGCAGGCCTGACACCATTGACGTGAAGCAGATGAAGGCACAGGCCCGGGAGGAGAAGCACCAGAAGCAGATGGAGCGTG
CTATGCTGGAAAATGAGAAGAAGAAGAAGCGTGAAATGGCAGAAAAGGAGAAAGAAGATTGAACGGGAGAAGGAGGAGCT
GATGGAGAGGCTGAAGCAGATCGAGGAGCAGACTAAGAAGGCTCAGCAAGAACTGGAAGAACAGACCCATAGGGCTCTGG
AACTTCAGCAGGAATGGAAGCATGCCCAGAGAGAGGCTGAAAAGCTGACCAAGGAGCGTCAAGAAGCTGAAGAGGCCAAG
GAGGTCTTGCTGCAGGCCTCCCGGGACCAGAAAAAGACTCAGGAAAAGCTGGCCTTGGAAATGGCAGAGCTGACAGCTCA
AATCTCCCAGCTGGAGATGGCCCTACAGAAGAAAGAGAGAGAGGCTGTGGAGTGGCAGCAGAAGGCCCAGATGGTATAGG
AAGACTTGGAGAAGACCCGTGTTGAGCTGAAGACTGCCATGAGTACACCTCTGTGGCACAGCCTGCTGAGAATGAGTAGG
ATGAGCAGGATGAGAATGGGGCAGAGGCTAGTGCTGACCTAGGGGCTGATGCTATGGCCAAGGACCGCAGTGAGGAGGAA
CGTACCACTGAGGCAGAGAAGAATGAGCGTGTGCAGAAGCACCTGAAGGCCCTCACTTCGGAGCTGGCCAGTGCCGGAGA
TGAGTCCAAGAAGACTGCCAATGACATGATCCATGCTGAGAACATGCAACTGGGCCGAGATGAATACAAGACCATGCGCC
AGATCCAGCAGGGCAACAACAAGCAGCACATTGATGAATTTGAGTCC

Alignment

ORF - retro_pabe_2623 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.16 %
• Parental protein coverage: 99.83 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MPKTISVRVTTMDAELEFAIQPNTTGKQLFDQVVKTIGLREVWFFGLQYQDTKGFSTWLKLNKKVTAQDV
          MPKT.SV.VTTMDAELEFAIQPNTTGKQLFDQVVKTIGLREVWFFGLQYQDTKGFSTWLKLNKKVTAQDV
Retrocopy MPKTTSVGVTTMDAELEFAIQPNTTGKQLFDQVVKTIGLREVWFFGLQYQDTKGFSTWLKLNKKVTAQDV

Parental  RKESPLLFKFRAKFYPEDVSEELIQDITQRLFFLQVKEGILNDDIYCPPETAVLLASYAVQSKYGDFNKE
          RKESPLLFKF.AKFYPEDVSEELIQDITQRLFFLQVK.GILNDDIYCPPETAVLLASYAV.SKYG.FNKE
Retrocopy RKESPLLFKFSAKFYPEDVSEELIQDITQRLFFLQVKQGILNDDIYCPPETAVLLASYAVLSKYGNFNKE

Parental  VHKSGYLAGDKLLPQRVLEQHKLNKDQWEERIQVWHEEHRGMLREDAVLEY-LKIAQDLEMYGVNYFSIK
          VHKSGYLAGDKLLPQRVLEQHKLNKDQWEERIQVWHEEH.GML.EDAVLEY.LKI.Q.LEMYGVNYFSIK
Retrocopy VHKSGYLAGDKLLPQRVLEQHKLNKDQWEERIQVWHEEHGGMLGEDAVLEY<LKITQNLEMYGVNYFSIK

Parental  NKKGSELWLGVDALGLNIYEQNDRLTPKIGFPWSEIRNISFNDKKFVIKPIDKKAPDFVFYAPRLRINKR
          NK.GSELWLGVDALGLNIYEQNDRLTP.IGFPWSEIR.ISFNDKKFVIKPIDKKAPD.VFY.P.LRINK.
Retrocopy NKTGSELWLGVDALGLNIYEQNDRLTPNIGFPWSEIRSISFNDKKFVIKPIDKKAPDLVFYVPWLRINKW

Parental  ILALCMGNHELYMRRRKPDTIEVQQMKAQAREEKHQKQMERAMLENEKKKREMA-EKEKEKIEREKEELM
          ILALCMGNHELYMRR..PDTI.V.QMKAQAREEKHQKQMERAMLENEKKK......K...KIEREKEELM
Retrocopy ILALCMGNHELYMRRCRPDTIDVKQMKAQAREEKHQKQMERAMLENEKKKKREM>QKRRKKIEREKEELM

Parental  ERLKQIEEQTKKAQQELEEQTRRALELEQERKRAQSEAEKLAKERQEAEEAKEALLQASRDQKKTQEQLA
          ERLKQIEEQTKKAQQELEEQT.RALEL.QE.K.AQ.EAEKL.KERQEAEEAKE.LLQASRDQKKTQE.LA
Retrocopy ERLKQIEEQTKKAQQELEEQTHRALELQQEWKHAQREAEKLTKERQEAEEAKEVLLQASRDQKKTQEKLA

Parental  LEMAELTARISQLEMARQKKESEAVEWQQKAQMVQEDLEKTRAELKTAMSTP-HVAEPAENEQDEQDENG
          LEMAELTA.ISQLEMA.QKKE.EAVEWQQKAQMV.EDLEKTR.ELKTAMSTP..VA.PAENE.DEQDENG
Retrocopy LEMAELTAQISQLEMALQKKEREAVEWQQKAQMV*EDLEKTRVELKTAMSTP<SVAQPAENE*DEQDENG

Parental  AEASADLRADAMAKDRSEEERTTEAEKNERVQKHLKALTSELANARDESKKTANDMIHAENMRLGRDKYK
          AEASADL.ADAMAKDRSEEERTTEAEKNERVQKHLKALTSELA.A.DESKKTANDMIHAENM.LGRD.YK
Retrocopy AEASADLGADAMAKDRSEEERTTEAEKNERVQKHLKALTSELASAGDESKKTANDMIHAENMQLGRDEYK

Parental  TLRQIRQGNTKQRIDEFES
          T.RQI.QGN.KQ.IDEFES
Retrocopy TMRQIQQGNNKQHIDEFES

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	0.06 RPM	49.43 RPM
SRP007412_cerebellum	0.00 RPM	18.48 RPM
SRP007412_heart	0.06 RPM	63.73 RPM
SRP007412_kidney	0.20 RPM	139.98 RPM
SRP007412_liver	0.06 RPM	65.33 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2623 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2623 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2623 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3153
Pan troglodytes	retro_ptro_2281
Gorilla gorilla	retro_ggor_1359

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000147065	1 retrocopy	retro_hsap_3153,
Gorilla gorilla	ENSGGOG00000001823	1 retrocopy	retro_ggor_1359,
Macropus eugenii	ENSMEUG00000015240	1 retrocopy	retro_meug_1267,
Oryctolagus cuniculus	ENSOCUG00000000149	1 retrocopy	retro_ocun_1173,
Pongo abelii	ENSPPYG00000020419	1 retrocopy	retro_pabe_2623 ,
Tursiops truncatus	ENSTTRG00000002946	1 retrocopy	retro_ttru_173,