RetrogeneDB ID: retro_pabe_1916

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 22:41211692..41212415(-)
• Located in intron of: ENSPPYG00000011937

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRNT1
• Ensembl ID: ENSPPYG00000013702
• Aliases: None
• Description: tRNA nucleotidyl transferase, CCA-adding, 1 [Source:HGNC Symbol;Acc:17341]

Sequence

>retro_pabe_1916
AGAGTACAATACAATTGTTTTTGAATTTTAAGATATGTCAGGTTTTGTGGGAGAACTGTAGACAAACCTGGTGACCACGG
TCCTGAGAAGCAACTGCAGAGCCTGCAAAAGGCCTGGCTGGGCTATTAGGAGAAAGCATTTGGGTGGAACTAAAAAAGCT
CTTGACAGTAAACATGTAAATCATTTGATTCACCTTATCTATGATCTTCATGTGGCTCCTTATGTAGGTGTAACTGCCAA
TGCAAGTTTAGAAGAATTTAACAAAGTCAGTAAAAATGTCGAAGGTTTTTCACCAAAGCCAATGACTCTTTTGGCCTCAT
TATTCAAAGTACAGAATGATGTCACAAAATTGGATTGGAGGTTGACGATTTGAAAAGAAGAGAAAAACCTTGGCTTATTT
ATAGTTAAAAATAAAAAAGACTGAATTAAAGCAATAGATAGTTCAGAACCACTGAAACCCTATCAAGACTTTCTTAGGGA
CTTTAGGGAACTTGCCGTGACTTCTCACATACGTGAACTACTGAAGAGTCAAGGAGAGCACCATCCCCTAAAGAAAGGGC
AGCTGTGGTCCCTTCCTACAGTTCCTGTTCAGTGGGCACGACACCAGAAAAGTGGACATTTCTTGGGGGAAAAGAAACCA
GGGCTCTATTACAACAACTACAAGAACGGTGGAGAAAAAGTGGTTACCAAGGGGAAAAAGATAAACTTCTAAGTTACCTA
AAG

Alignment

ORF - retro_pabe_1916 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.56 %
• Parental protein coverage: 55.99 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RIQEDYLRILRYFRFYGRIVDKPGDHDPE-TLEAI-AENAKGLAGISGERIWVELKKILVGN-HVNHLIH
          R.Q.....ILRY.RF.GR.VDKPGDH.PE..L....A....GL.G...E.IWVELKK.L..N.HVNHLIH
Retrocopy RVQYNCF*ILRYVRFCGRTVDKPGDHGPEKQLQSL<AKGLAGLLG---ESIWVELKKLLTVN<HVNHLIH

Parental  LIYDLDVAPYIGLPANASLEEFDKVSKNVEGFSPKPMTLLASLFKVQDDVTKLDLRLKIAKEEKNLGLFI
          LIYDL.VAPY.G..ANASLEEF.KVSKNVEGFSPKPMTLLASLFKVQ.DVTKLD.RL.I.KEEKNLGLFI
Retrocopy LIYDLHVAPYVGVTANASLEEFNKVSKNVEGFSPKPMTLLASLFKVQNDVTKLDWRLTI*KEEKNLGLFI

Parental  VKNKKDLIKATDSSEPLKPYQDFIIDSREPDAPTRVCELLKYQGEHCLLKEMQQWSIPPFPV-SGHDIRK
          VKNKKD.IKA.DSSEPLKPYQDF..D.RE........ELLK.QGEH..LK..Q.WS.P..PV.SGHD.RK
Retrocopy VKNKKD*IKAIDSSEPLKPYQDFLRDFRELAVTSHIRELLKSQGEHHPLKKGQLWSLPTVPV>SGHDTRK

Parental  VGIS-SGKEIGALLQQLREQWKKSGYQMEKDELLSYIK
          V.IS..GKE..ALLQQL.E.W.KSGYQ.EKD.LLSY.K
Retrocopy VDIS>GGKETRALLQQLQERWRKSGYQGEKDKLLSYLK

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	4.92 RPM
SRP007412_cerebellum	0.00 RPM	5.11 RPM
SRP007412_heart	0.00 RPM	2.20 RPM
SRP007412_kidney	0.03 RPM	5.67 RPM
SRP007412_liver	0.00 RPM	2.72 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1916 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1916 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1916 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2598
Pan troglodytes	retro_ptro_1522

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015466	1 retrocopy	retro_cjac_1512,
Dasypus novemcinctus	ENSDNOG00000008837	1 retrocopy	retro_dnov_1635,
Echinops telfairi	ENSETEG00000018177	2 retrocopies	retro_etel_1871, retro_etel_905,
Homo sapiens	ENSG00000072756	2 retrocopies	retro_hsap_246, retro_hsap_2598,
Gorilla gorilla	ENSGGOG00000015286	1 retrocopy	retro_ggor_300,
Nomascus leucogenys	ENSNLEG00000003226	1 retrocopy	retro_nleu_856,
Petromyzon marinus	ENSPMAG00000002236	1 retrocopy	retro_pmar_17,
Pongo abelii	ENSPPYG00000013702	3 retrocopies	retro_pabe_1916 , retro_pabe_2721, retro_pabe_412,
Pan troglodytes	ENSPTRG00000014564	1 retrocopy	retro_ptro_1522,