RetrogeneDB ID: retro_pabe_1415

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 16_random:10258955..10260429(+)
• 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_1415
ATGAATGCTGGGGCAGAAGCCGAGTTCAACATCCTCCTGGCTACCGACTCCTACAAGGTTACTCACTATAAACAATATCC
ACCCAACACAAGCAAAGTTTATTCCTACTTTGAATGCTGTGAAAAGAAGACAGAAAATTCCAAAATTAAAGAAGGTGAAA
TACGAGGAAACAGTACTTTATGGGTTGCCATACATTCTTAATAAGTACTTAAAAGGTAAAGTAGTAGCCAAAGAGAAAAT
CCAGGGAGCCAAAGAGGTCTACAAAGAACATTTCCATGATGATGTCTTTAATGAAAAGGGATGGGACTACATTCCTAAGA
AATATGATGGGCATCTTCCAATAGAAGTAAAAGCTGTTCCCGCGGGCTCTGTCACTCCCAGAGGAAATGTTCTCTTCACG
GTGGAAAACACAGATCCAAAGTGTTACTGGCTTACAAATTGGATTAAGACTATCCTTGTTCAGTCCTGGTATCTAACCAC
AGTGGCCACAAATTCTAGAGAGCAGAAGAAAATATTGGCCAAATGTTTGTTAGAAACTTCTGGTAACTTAGATGGTCTGG
AATACAAGTTACATGATTTTGGCTACAGAGGAGCCTCTTCCCAGGAGACTGCTGGCATAGGAGCATCTGCTCATTTGGTT
AACTTCAAAGGAACAGATACAGTAGCAGGAATTGCTCTAATTAAAAAAATATTATGGAACGAAAGATCCTGTTCCAGGCT
ATTCTGTTCCAGCAGCAGAACACAGTACCATAAGAGCTTGGGGGAAAGACCATGAAAAAGATGCTTTTGAACATATAGTA
ACACAGTTTTCATCAGTGCCTGTATCTGTGGTCAGCGATAGCTATGACATCTATAATAAGTATGAGAAAATATGGGGTGA
AGATCTAAGACATTTAATAGTATCGAGAAGTACAGAGGCACCACTAATCATCAGACCTGATTCTGGAAACCCTCATGACA
CTGTGTTAAAGGTTTTGGAGATTTTAGTAAGAAGTTTCCTGTTACTGAGAACTCAAAGGGCTACAAGTTGCTGCCACCTT
ATCTTAGAGTTATTCAAGGGGATGGAGTAGTTATTAATACCTTACAAGAGATTGTAGAAGGCATGAAACAAAAAAAGGTG
GAGTATTGAAAATGTTTCCTTCAGTTCTGGTGGAGCTTTGCTACAGAAGTTAACAAGAGATCTCTTGAATTGTTCCTTCA
AGTGTGGTTATGTTGTAACCAATGGCCTTGGGATTAACGTCTTCAAGGACCCAGTTGCTGATCCCAACAAAAGTTCCAGA
AGGGCCGATTATCTTTACATAGAACGCCAGCAGGGAATTTTGTTACACTGGAGGAAGGAATAGGAGACCTTGAGGAATAT
GGTCATGATCTTCTCCATACTGTCTTCAAGAATGGCAATGTGACAAAAAGCTGTTCATTTGATGAAGTAAGAAAAAATGC
ACAGGTGAATATTGAACTGGAAGCAGCACCTCAT

Alignment

ORF - retro_pabe_1415 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.12 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MNAAAEAEFNILLATDSYKVTHYKQYPPNTSKVYSYFECREKKTENSK-LRKVKYEETVFYGLQYILNKY
          MNA.AEAEFNILLATDSYKVTHYKQYPPNTSKVYSYFEC.EKKTENSK.L.KVKYEETV.YGL.YILNKY
Retrocopy MNAGAEAEFNILLATDSYKVTHYKQYPPNTSKVYSYFECCEKKTENSK>LKKVKYEETVLYGLPYILNKY

Parental  LKGKVVTKEKIQEAKDVYKEHFQDDVFNEKGWNYILEKYDGHLPIEIKAVPEGFVIPRGNVLFTVENTDP
          LKGKVV.KEKIQ.AK.VYKEHF.DDVFNEKGW.YI..KYDGHLPIE.KAVP.G.V.PRGNVLFTVENTDP
Retrocopy LKGKVVAKEKIQGAKEVYKEHFHDDVFNEKGWDYIPKKYDGHLPIEVKAVPAGSVTPRGNVLFTVENTDP

Parental  ECYWLTNWIETILVQTWYPITVATNSREQKKILAKYLLETSGNLDGLEYKLHDFGYRGVSSQETAGIGAS
          .CYWLTNWI.TILVQ.WY..TVATNSREQKKILAK.LLETSGNLDGLEYKLHDFGYRG.SSQETAGIGAS
Retrocopy KCYWLTNWIKTILVQSWYLTTVATNSREQKKILAKCLLETSGNLDGLEYKLHDFGYRGASSQETAGIGAS

Parental  AHLVNFKGTDTVAGIALIKK-YYGTKDPVPGYSVPAAEHSTITAWGKDHEKDAFEHIVTQFSSVPVSVVS
          AHLVNFKGTDTVAGIALIKK.YYGTKDPVPGYSVPAAEHSTI.AWGKDHEKDAFEHIVTQFSSVPVSVVS
Retrocopy AHLVNFKGTDTVAGIALIKK>YYGTKDPVPGYSVPAAEHSTIRAWGKDHEKDAFEHIVTQFSSVPVSVVS

Parental  DSYDIYNACEKIWGEDLRHLIVSRSTAAPLIIRPDSGNPLDTVLKVLEIL-GKKFPVTENSKGYKLLPPY
          DSYDIYN..EKIWGEDLRHLIVSRST.APLIIRPDSGNP.DTVLKVLEIL..KKFPVTENSKGYKLLPPY
Retrocopy DSYDIYNKYEKIWGEDLRHLIVSRSTEAPLIIRPDSGNPHDTVLKVLEIL<SKKFPVTENSKGYKLLPPY

Parental  LRVIQGDGVDINTLQEIVEGMKQ-KMWSIENIAFGSGGGLLQKLTRDLLNCSFKCSYVVTNGLGINVFKD
          LRVIQGDGV.INTLQEIVEGMKQ.K.WSIEN..F.SGG.LLQKLTRDLLNCSFKC.YVVTNGLGINVFKD
Retrocopy LRVIQGDGVVINTLQEIVEGMKQ>KRWSIENVSFSSGGALLQKLTRDLLNCSFKCGYVVTNGLGINVFKD

Parental  PVADPNKRSK-KGRLSLHRTPAGNFVTLEEGKGDLEEYGHDLLHTVFKNGKVTKSYSFDEIRKNAQLNIE
          PVADPNK.S..KGRLSLHRTPAGNFVTLEEG.GDLEEYGHDLLHTVFKNG.VTKS.SFDE.RKNAQ.NIE
Retrocopy PVADPNKSSR<KGRLSLHRTPAGNFVTLEEGIGDLEEYGHDLLHTVFKNGNVTKSCSFDEVRKNAQVNIE

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	0.15 RPM	299.92 RPM
SRP007412_kidney	0.03 RPM	121.95 RPM
SRP007412_liver	0.31 RPM	680.64 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1415 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1415 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1415 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,