RetrogeneDB ID: retro_ptro_1522

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 22:44601746..44602469(-)
• Located in intron of: ENSPTRG00000014500

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRNT1
• Ensembl ID: ENSPTRG00000014564
• Aliases: None
• Description: None

Sequence

>retro_ptro_1522
AGAGTACAATACAATTGTTTTTGAATTTTAAGATATGTCAGGTTTTGTGGGAGAACTGTAGACAAACCTGGTGACCACGG
TCCTGAGAAGCAACTGCAGAGCCTGCAAAAGGCCTGGCTGGGCTATTAGGAGAAAGCATTTGGGTGGAACTAAAAAAGCT
CTTGTCAGTAAACATGTAAATCATTTGATTCACCTTATCTATGATCTTCATGTGGCTCCTTATGTAGGTATAACAGCCAA
TGCAAGTTTAGAAGAATTTAACAAAGTCAGTAAAAATGTCAAAGGTTTTTCACCAAAGCCAATGACTCTTTTGGCCTCAT
TATTCAAAGTACAGAATGATGTCACAAAATTGGATTGGAGGTTGACGACTTCAAAAGAAGAGAAAAACCTTGGCTTGTTT
ATAGTTAAAAATAAAAAAGACTGAATTAAAGCAATAGATAGTTCAGAGCCACTGAAACCCTACCAAGACTTTCTCAGGGA
CTTTAGGGAACTTGCCGTGACTTCTCACATACGTGAACTACTGAAGAGCCAAGGAGAGCACCATCCCCTAAAGGAAAGGC
AGCTGTGGTCCCTTCCTACAGTTCCTGTTCTGTGGGCATGACACCAGAAAAGTGGACATTTCTTGGGGGAAAAGAAACCA
GGGCTCTATTACAACAACTACAAGAATGGTGGAGAAAAAGTGGTTACCAAGGGGGAAAAGATAAACTTCTAAGTTATCTG
AAG

Alignment

ORF - retro_ptro_1522 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.95 %
• Parental protein coverage: 55.99 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RIQEDYLRILRYFRFYGRIVDKPGDHDPE-TLEAI-AENAKGLAGISGERIWVELKKI-LVGNHVNHLIH
          R.Q.....ILRY.RF.GR.VDKPGDH.PE..L....A....GL.G...E.IWVELKK..LV..HVNHLIH
Retrocopy RVQYNCF*ILRYVRFCGRTVDKPGDHGPEKQLQSL<AKGLAGLLG---ESIWVELKKL<LVSKHVNHLIH

Parental  LIYDLDVAPYIGLPANASLEEFDKVSKNVDGFSPKPMTLLASLFKVQDDVTKLDLRLKIAKEEKNLGLFI
          LIYDL.VAPY.G..ANASLEEF.KVSKNV.GFSPKPMTLLASLFKVQ.DVTKLD.RL...KEEKNLGLFI
Retrocopy LIYDLHVAPYVGITANASLEEFNKVSKNVKGFSPKPMTLLASLFKVQNDVTKLDWRLTTSKEEKNLGLFI

Parental  VKNRKDLIKATDSSDPLKPYQDFIIDSREPDATTRVCELLKYQGEHCLLKEMQQWSIPPFPV-SGHDIRK
          VKN.KD.IKA.DSS.PLKPYQDF..D.RE...T....ELLK.QGEH..LKE.Q.WS.P..PV..GHD.RK
Retrocopy VKNKKD*IKAIDSSEPLKPYQDFLRDFRELAVTSHIRELLKSQGEHHPLKERQLWSLPTVPV>CGHDTRK

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

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	0.04 RPM	10.12 RPM
SRP007412_cerebellum	0.00 RPM	7.85 RPM
SRP007412_heart	0.00 RPM	5.57 RPM
SRP007412_kidney	0.03 RPM	9.70 RPM
SRP007412_liver	0.03 RPM	6.71 RPM
SRP007412_testis	0.00 RPM	25.19 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1522 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1522 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1522 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2598
Pongo abelii	retro_pabe_1916

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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 ,