RetrogeneDB ID: retro_pabe_1407

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 16_random:5288240..5289714(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000018270
• Aliases: None
• Description: None

Sequence

>retro_pabe_1407
ATGAATGCTGGGGCAGAAGCCGAGTTCAACATCCTCCTGGCTACCGACTCCTGCAAGGTTACTCTCTATAAACAATATCC
ACCCAACACAAGCAAAGTTTATTCCTACTTTGAATGCTGTGAAAAGAAGACAGAAAATTCCAAAATTAAGGAAGGCGAAA
TACAAGGAAACAGTACTTTATGGGTTGCCGTACATTCTTAATAAGTACTTTAAAGGTAAAGTAGTAGCCAAAGAGAAAAT
CCAGGGAGCCAAAGAGGTCTACAAAGAACATTTCCAAGATGATGTCTTTAATGAAAAGGGATGGGACTACATTCCTAAGA
AATATGATGGGCATCTTCCAATAGAAGTAAAAGCTGTTCCCGAGGGCTCTGTCACTCCCAGAGGAAATGTTCTCTTCACG
GTGGAAAACACAGATCCAAAGTGTTACTGGCTTACAAATTGGATTGAGACTATCCTTGTTCAGTCCTGGTATCTAACCAC
AGTGGCCACAAATTCTAGAGAGCAGAAGAAAATATTGGCCAAATGTTTGTTAGAAACTTCTGGTAACTTAGATGGTCTGG
AATACAAGTTACATGATTTTGGCTACAGAGGAGCCTCTTCCTAAGAGACTGCTGGCATAGGAGCATCTGCTCATTTGGTT
AACTTCAAAGGAACAGATACAGTAGCAGGAATTGCTCTAATTAAAAAAATATTATGGAACGAAAGATCCTGTTCCAGGCT
GTTCTTTTCCAGCAGCAGAACACAGTACCGTAACAGCTTGGGGGAAAGACCATGAAAAAGATGCTTTTGAACATATAGTA
ACACAGTTTTCATCAGTGCCTGTATCTGTGGTCAGCAATAGCTATGACATCTATAATAAGTGTGAGAAAATATGGGGTGA
AGATCTAAGACATTTAATAGTATCGAGAAGTACAGAGGCACCACTAATAATCAGACCTGATTCTGGAAACCCTCTTGACA
CTGTGTTAAAGGTTTTGGAGATTTTAGTAAGAAGTTTCCTGTTACTGAGAACTCAAAGGGCTACAAGTTGCTGCCACCTT
ATCTTAGAGTTATTCAAGGGGATGGAGTAGTTATTAATACCTTACAAGAGATTGTAGAAGGCATGAAACAAAAAAAGGTG
GAGTATTGAAAATGTTTCCTTCGGTTCTGGTGGAGCTTTGCTACAGAAGTTAACAAGAGATCTCTTGAATTGTTCCTTCA
AGTGTGGTTATGTTGTAACCAATGGCCTTGGGATTAACGTCTTCAAGGACCCAGTTGCTGATCCCAACAAAAGTTCCAGA
AGGGCCGATTATCTTTACATAGAACGCCAGCAGGGAATTTTGTTACACTGGGGGAAGGAATAGGAGACCTTGAGGAATAT
GGTCATGATCTTCTCCATACTGTCTTCAAGAATGGCAATGTGACAAAAAGCTGTTCATTTGATGAAGTAAGAAAAAATGC
ACAGGTGAATATTGAACTGGAAGCAGCACCTCAT

Alignment

ORF - retro_pabe_1407 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.52 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MNAAAEAEFNILLATDSYKVTHYKQYPPNTSKVYSYFECREKKTENSK-LRKVKYEETVFYGLQYILNKY
          MNA.AEAEFNILLATDS.KVT.YKQYPPNTSKVYSYFEC.EKKTENSK.LRK.KY.ETV.YGL.YILNKY
Retrocopy MNAGAEAEFNILLATDSCKVTLYKQYPPNTSKVYSYFECCEKKTENSK>LRKAKYKETVLYGLPYILNKY

Parental  LKGKVVTKEKIQEAKDVYKEHFQDDVFNEKGWNYILEKYDGHLPIEIKAVPEGFVIPRGNVLFTVENTDP
          .KGKVV.KEKIQ.AK.VYKEHFQDDVFNEKGW.YI..KYDGHLPIE.KAVPEG.V.PRGNVLFTVENTDP
Retrocopy FKGKVVAKEKIQGAKEVYKEHFQDDVFNEKGWDYIPKKYDGHLPIEVKAVPEGSVTPRGNVLFTVENTDP

Parental  ECYWLTNWIETILVQTWYPITVATNSREQKKILAKYLLETSGNLDGLEYKLHDFGYRGVSSQETAGIGAS
          .CYWLTNWIETILVQ.WY..TVATNSREQKKILAK.LLETSGNLDGLEYKLHDFGYRG.SS.ETAGIGAS
Retrocopy KCYWLTNWIETILVQSWYLTTVATNSREQKKILAKCLLETSGNLDGLEYKLHDFGYRGASS*ETAGIGAS

Parental  AHLVNFKGTDTVAGIALIKK-YYGTKDPVPGYSVPAAEHSTITAWGKDHEKDAFEHIVTQFSSVPVSVVS
          AHLVNFKGTDTVAGIALIKK.YYGTKDPVPG.S.PAAEHST.TAWGKDHEKDAFEHIVTQFSSVPVSVVS
Retrocopy AHLVNFKGTDTVAGIALIKK>YYGTKDPVPGCSFPAAEHSTVTAWGKDHEKDAFEHIVTQFSSVPVSVVS

Parental  DSYDIYNACEKIWGEDLRHLIVSRSTAAPLIIRPDSGNPLDTVLKVLEIL-GKKFPVTENSKGYKLLPPY
          .SYDIYN.CEKIWGEDLRHLIVSRST.APLIIRPDSGNPLDTVLKVLEIL..KKFPVTENSKGYKLLPPY
Retrocopy NSYDIYNKCEKIWGEDLRHLIVSRSTEAPLIIRPDSGNPLDTVLKVLEIL<SKKFPVTENSKGYKLLPPY

Parental  LRVIQGDGVDINTLQEIVEGMKQ-KMWSIENIAFGSGGGLLQKLTRDLLNCSFKCSYVVTNGLGINVFKD
          LRVIQGDGV.INTLQEIVEGMKQ.K.WSIEN..FGSGG.LLQKLTRDLLNCSFKC.YVVTNGLGINVFKD
Retrocopy LRVIQGDGVVINTLQEIVEGMKQ>KRWSIENVSFGSGGALLQKLTRDLLNCSFKCGYVVTNGLGINVFKD

Parental  PVADPNKRSK-KGRLSLHRTPAGNFVTLEEGKGDLEEYGHDLLHTVFKNGKVTKSYSFDEIRKNAQLNIE
          PVADPNK.S..KGRLSLHRTPAGNFVTL.EG.GDLEEYGHDLLHTVFKNG.VTKS.SFDE.RKNAQ.NIE
Retrocopy PVADPNKSSR<KGRLSLHRTPAGNFVTLGEGIGDLEEYGHDLLHTVFKNGNVTKSCSFDEVRKNAQVNIE

Parental  LEAAHH
          LEAA.H
Retrocopy LEAAPH

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	52.25 RPM
SRP007412_cerebellum	0.00 RPM	50.46 RPM
SRP007412_heart	0.12 RPM	299.92 RPM
SRP007412_kidney	0.03 RPM	121.95 RPM
SRP007412_liver	0.18 RPM	680.64 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1407 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1407 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1407 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016193	2 retrocopies	retro_cjac_1281, retro_cjac_3877,
Cavia porcellus	ENSCPOG00000009226	1 retrocopy	retro_cpor_848,
Homo sapiens	ENSG00000105835	1 retrocopy	retro_hsap_79,
Oryctolagus cuniculus	ENSOCUG00000013417	1 retrocopy	retro_ocun_777,
Pongo abelii	ENSPPYG00000018270	2 retrocopies	retro_pabe_1407 , retro_pabe_1415,
Pan troglodytes	ENSPTRG00000019571	1 retrocopy	retro_ptro_114,
Takifugu rubripes	ENSTRUG00000016695	1 retrocopy	retro_trub_33,