RetrogeneDB ID: retro_hsap_2598

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 22:46188293..46189016(-)
• Located in intron of: ENSG00000130638

Retrocopy information

• Ensembl ID: ENSG00000235347
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TRNT1
• Ensembl ID: ENSG00000072756
• Aliases: TRNT1, CCA1, MtCCA
• Description: tRNA nucleotidyl transferase, CCA-adding, 1 [Source:HGNC Symbol;Acc:17341]

Sequence

>retro_hsap_2598
AGAGTACAATACAATTGTTTTTGAATTTTAAGATATGTCAGGTTTTGTGGGAGAACTGTAGACAAACCTGGTGACCACGG
TCCTGAGAAGCAACTGCAGAGCCTGCAAAAGGCCTGGCTGGGCTATTAGGAGAAAGCATTTGGGTGGAACTAAAAAAGCT
CTTGTCAGTAAACATGTAAATCATTTGATTCACCTTATCTATGATCTTCATGTGGCTCCCTATGTAGGTATAACAGCCAA
TGCAAGTTTAGAAGAATTTAACAAAGTCAGTAAAAATGTCGAAGGTTTTTCACCAAAGCCAATGACTCTTTTGGCCTCAT
TATTCAAAGTACAGAATGATGTCACAAAATTGGATTGGAGGTTGACGATTTCAAAAGAAGAGAAAAACCTTGGCTTGTTT
ATAGTTAAAAATAAAAAAGACTGAATTAAAGCAATAGATAGTTCAGAGCCACTGAAACCCTACCAAGACTTTCTCAGGGA
CTTTAGGGAACTTGCCGTGACTTCTCACATACGTGAACTACTGAAGAGCCAAGGAGAGCACCATCCCCTAAAGGAAAGGC
AGCTGTGGTCCCTTCCTACAGTTCCTGTTCAGTGGGCATGACACCAGAAAAGGGGACATTTCTTGGGGGAAAAGAAACCA
GGGCTCTATTACAACAACTACAAGAACGGTGGAGAAAAAGTGGTTACCAAGGGGGAAAAGATAAACTTCTAAGTTATCTG
AAG

Alignment

ORF - retro_hsap_2598 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  LIYDLDVAPYIGLPANASLEEFDKVSKNVDGFSPKPVTLLASLFKVQDDVTKLDLRLKIAKEEKNLGLFI
          LIYDL.VAPY.G..ANASLEEF.KVSKNV.GFSPKP.TLLASLFKVQ.DVTKLD.RL.I.KEEKNLGLFI
Retrocopy LIYDLHVAPYVGITANASLEEFNKVSKNVEGFSPKPMTLLASLFKVQNDVTKLDWRLTISKEEKNLGLFI

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

Parental  VGIS-SGKEIGALLQQLREQWKKSGYQMEKDELLSYIK
          ..IS..GKE..ALLQQL.E.W.KSGYQ..KD.LLSY.K
Retrocopy GDIS>GGKETRALLQQLQERWRKSGYQGGKDKLLSYLK

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
bodymap2_adipose	0.00 RPM	12.96 RPM
bodymap2_adrenal	0.00 RPM	22.68 RPM
bodymap2_brain	0.00 RPM	14.63 RPM
bodymap2_breast	0.00 RPM	16.95 RPM
bodymap2_colon	0.00 RPM	17.03 RPM
bodymap2_heart	0.00 RPM	9.82 RPM
bodymap2_kidney	0.00 RPM	30.19 RPM
bodymap2_liver	0.00 RPM	8.03 RPM
bodymap2_lung	0.12 RPM	13.73 RPM
bodymap2_lymph_node	0.00 RPM	20.72 RPM
bodymap2_ovary	0.00 RPM	22.32 RPM
bodymap2_prostate	0.16 RPM	20.97 RPM
bodymap2_skeletal_muscle	0.00 RPM	6.42 RPM
bodymap2_testis	0.04 RPM	19.95 RPM
bodymap2_thyroid	0.00 RPM	21.52 RPM
bodymap2_white_blood_cells	0.00 RPM	18.68 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2598 was not detected

EST

No EST(s) were mapped for retro_hsap_2598 retrocopy.

TSS

No TSS is located nearby retro_hsap_2598 retrocopy 5' end.

Lab

retro_hsap_2598 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2598 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1522
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,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.09 RPM
CEU_NA11843	0.03 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.11 RPM
CEU_NA12400	0.04 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.09 RPM
CEU_NA12827	0.05 RPM
CEU_NA12872	0.03 RPM
CEU_NA12873	0.06 RPM
FIN_HG00183	0.11 RPM
FIN_HG00277	0.04 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.06 RPM
FIN_HG00328	0.05 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.03 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.03 RPM
GBR_HG00111	0.09 RPM
GBR_HG00114	0.05 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.05 RPM
GBR_HG00134	0.02 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.03 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.02 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.14 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.03 RPM
TSI_NA20765	0.06 RPM
TSI_NA20771	0.06 RPM
TSI_NA20786	0.03 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.10 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.06 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.03 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.02 RPM
YRI_NA19213	0.02 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.00 RPM

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Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).