RetrogeneDB ID: retro_pabe_2269

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:173504405..173505542(+)
• Located in intron of: ENSPPYG00000014284

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM20B
• Ensembl ID: ENSPPYG00000000466
• Aliases: None
• Description: family with sequence similarity 20, member B [Source:HGNC Symbol;Acc:23017]

Sequence

>retro_pabe_2269
ATACATCAACTGCCAAGCGGCGTTTCACCACTTGATCACCTGAGGGCTTTTCACCGAATGATGACTGGCTAGTGGATGGA
GCTGTCACCCAAGTTGGACCACATGTTGCAGTCTTCCTAGGAGATTGCAGCCCAGTGGGTGGTTCCCCAGGAAGTGTACT
GTGAAGAGACACCAGAGCTGGGGGCAATCATGCATGCCATGGCCACCAAGCAAATTATTAAAGCTGATGTGGGTTATAAA
GGGACACAGCTGAAAGCCTTACTGATCCTTGAAAGGGAACAGAAAGTTGTTTTCGAACCTAAGTAGTATAGCCGAGACTA
TGTAGTGGAAGGGAACCATATGCCGGTTATGATACACACAATGCAGAGGTAGCAGCCTTTCACTTGGACAGGATTGTGGG
TGTCCCAGAGCACTGTTGATGGTGGGCAGATTTGTTCATCTTCAGACAGAGTTCAAGCCTGTTACCATGGAGCAGCTGTT
GAGCCCCTTCCTAACTGTAGGAAACAATACTTCTTTTTATGGGAAATGTTATTACTACCAAGAAACAGAATCAGCTTGTG
CCGATGGAGACACAATGGAAAAATCTGTCACACTTTGGCTTCCAGATGTGTGGCCTCTCCAGAAACACTGACATCCGTGG
GCCAGGACTTACTGAAAAGGCAAATTGGCCAGGTGGGAGTATGATGAGAGCTACTGTGAGGCTGTGAAGAAAACGTCCCT
TTATGACTCTGGCCTGTGCCGCTTGGACACCATTAACACAGCTGTCTTTGATTACCTGATGGACAATGCTGACTGCCATT
ACTATAAGAACTTTCAAGATAATGAGGGTGCCAGTATGCTCATCCTTCTTGATAACGACAAAAGCTTTGGGAACCCCCTG
CTGGATGAAAGAAGCATTCTTTCCCCCCTCTATCAGTGTGGCATCACTCAGGTTTCTACCTGGAACAAACGGAACTACCT
AAAGAACGGTGTGCTGAAGTCTACCTTAAAATCTGCCATGGCCCATGACCCCCTCTACCCAGTGCTCTCTGATCCTTGTC
TGGACACCATGGACCAGTGGCTCCTGAGTGTCCTGGCCACCATGGAGCAGTGCACTGACCAGTTTGGGATGGACACTGTA
TGGTGGAAGACACAATG

Alignment

ORF - retro_pabe_2269 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.33 %
• Parental protein coverage: 92.91 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  IDNLDTSAANREDQRAFHRMMTGLRVELAPKLDHTLQSPWEIAAQWVVPREVYPEETPELGAIMHAMATK
          I..L..........RAFHRMMTG...EL.PKLDH.LQS..EIAAQWVVP.EVY.EETPELGAIMHAMATK
Retrocopy IHQLPSGVSPLDHLRAFHRMMTG*WMELSPKLDHMLQSS*EIAAQWVVPQEVYCEETPELGAIMHAMATK

Parental  KIIKADVGYKGTQLKALLILEGGQKVVFKPKRYSRDYVVEG-EPYAGYDRHNAEVAAFHLDRILGFR-RA
          .IIKADVGYKGTQLKALLILE..QKVVF.PK.YSRDYVVEG.EPYAGYD.HNAEVAAFHLDRI.G...RA
Retrocopy QIIKADVGYKGTQLKALLILEREQKVVFEPK*YSRDYVVEG<EPYAGYDTHNAEVAAFHLDRIVGVP<RA

Parental  PLVVGRFVNLRTEIKPVATEQLLSTFLTVGNNTCFYGKCYYCRETEPACADGDTMEGSVTLWLPDVWPLQ
          .L.VGRFV.L.TE.KPV..EQLLS.FLTVGNNT.FYGKCYY..ETE.ACADGDTME.SVTLWLPDVWPLQ
Retrocopy LLMVGRFVHLQTEFKPVTMEQLLSPFLTVGNNTSFYGKCYYYQETESACADGDTMEKSVTLWLPDVWPLQ

Parental  KHRHPWGRTYREGKLARWEYDESYCDAVKKTSPYDSGPRLLDIIDTAVFDYLIGNADRHHYESFQDDEGA
          KH.HPW.RTY..GKLARWEYDESYC.AVKKTS.YDSG...LD.I.TAVFDYL..NAD.H.Y..FQD.EGA
Retrocopy KH*HPWARTY*KGKLARWEYDESYCEAVKKTSLYDSGLCRLDTINTAVFDYLMDNADCHYYKNFQDNEGA

Parental  SMLILLDNAKSFGNPSLDERSILAPLYQCCIIRVSTWNRLNYLKNGVLKSALKSAMAHDPISPVLSDPHL
          SMLILLDN.KSFGNP.LDERSIL.PLYQC.I..VSTWN..NYLKNGVLKS.LKSAMAHDP..PVLSDP.L
Retrocopy SMLILLDNDKSFGNPLLDERSILSPLYQCGITQVSTWNKRNYLKNGVLKSTLKSAMAHDPLYPVLSDPCL

Parental  DAVDQRLLSVLATVKQCTDQFGMDTV-LVEDRM
          D..DQ.LLSVLAT..QCTDQFGMDTV..VED.M
Retrocopy DTMDQWLLSVLATMEQCTDQFGMDTV<MVEDTM

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	68.45 RPM
SRP007412_cerebellum	0.00 RPM	58.98 RPM
SRP007412_heart	0.03 RPM	65.17 RPM
SRP007412_kidney	0.00 RPM	51.21 RPM
SRP007412_liver	0.00 RPM	28.31 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2269 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2269 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2269 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2730
Pan troglodytes	retro_ptro_1845

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005236	6 retrocopies	retro_chof_1509, retro_chof_1926, retro_chof_2615, retro_chof_2629, retro_chof_799, retro_chof_868,
Dasypus novemcinctus	ENSDNOG00000006175	2 retrocopies	retro_dnov_1484, retro_dnov_2346,
Echinops telfairi	ENSETEG00000005651	1 retrocopy	retro_etel_1128,
Homo sapiens	ENSG00000116199	1 retrocopy	retro_hsap_2730,
Gorilla gorilla	ENSGGOG00000002484	1 retrocopy	retro_ggor_1899,
Macropus eugenii	ENSMEUG00000006654	1 retrocopy	retro_meug_414,
Macaca mulatta	ENSMMUG00000006260	1 retrocopy	retro_mmul_1533,
Nomascus leucogenys	ENSNLEG00000015580	1 retrocopy	retro_nleu_592,
Otolemur garnettii	ENSOGAG00000012751	1 retrocopy	retro_ogar_2800,
Pongo abelii	ENSPPYG00000000466	2 retrocopies	retro_pabe_2268, retro_pabe_2269 ,
Pan troglodytes	ENSPTRG00000001725	1 retrocopy	retro_ptro_1845,
Ictidomys tridecemlineatus	ENSSTOG00000005086	2 retrocopies	retro_itri_441, retro_itri_539,
Tarsius syrichta	ENSTSYG00000005482	3 retrocopies	retro_tsyr_2065, retro_tsyr_2124, retro_tsyr_89,