RetrogeneDB ID: retro_hsap_4123

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 9:5110913..5112109(+)
• Located in intron of: ENSG00000096968

Retrocopy information

• Ensembl ID: ENSG00000236567
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TCF3
• Ensembl ID: ENSG00000071564
• Aliases: TCF3, E2A, E47, ITF1, TCF-3, VDIR, bHLHb21
• Description: transcription factor 3 [Source:HGNC Symbol;Acc:11633]

Sequence

>retro_hsap_4123
ATGAACCAGCCGCAGAGGATGGCATCCGTGGACACGGACAAGGAGCTCAGTAACCTGGACTTCAGCATGATGTTCCCGCT
GCCCGTTGCCAACGGGAAGGGCCGGCCCGCCTCCCTGGCCGGGGCGCAATTCAGAGGTTCAGGTCTTGAGAACTGGCCCA
GCTCAGGCTCCTGGGGCAGCGGCGACCAGAACAGCTCCTCCTTTGACCCCAGCTGGACGTTCAGCGAAGGCGCTCAACTT
GCTGAGTCGCACGGCAGCCACTCTCCATTCACATTCCTGGGACCGGGACTCGGAGGCAAGAGCAGCTAGCGCGGGCCTAT
TCCTCCTTTGGTAGAGACGCAGGCGTGCGCAGCCTGACTCAGGCTGGCTTCCTGCCGGGCAAGCTGGCCCTCAGCAGCCC
CGGACCCCTGTCCCCCTCAGGCATGAAGGGGACCTCCCGGTACTACCCCTCCTACGCCAGCAGCTCTGGCGGACAGAGGC
GGACAGCGGCCTGGACACGCAGCCCACGAAGGTCGGGAAGGTCCCGCCTGGTCTTCCATCCTCGGCGTACCTGCCCAGCT
CAGGTGAGGAGTACGGTAGGGATGCCGCCGCCTATCCATCCGCCAAGACGCCCAGCAGCGCCTGTCCCGCCCCCTTCTAC
ATGGCAGATGGCAGCCTGCACCCCTAAGCCGAGCTCTGGAGTTCCCTGGGCCAGGTGGGCTTTGGCCCCATGCTGGGCGG
GGGCTCATGCCCCTCGTCCCTCCCGCCCAGCAGCGGCCCTGTGGGCAGTGGCGGAGGCAGCAGCACGTTTGGCGGCCTGC
ACCAGCACGAGCGCGTGGGCTACCGGCTGCACGGAGGAGAAGTGAACGGTGGGCTTCCGGCTGCATCCACCTTCTCCTTG
GCCCCCGGAGCCACGTAGGCGGCGTCTCCAGCCACACGCCTGTCGGCGGGGCCGACAACCTCCTGGGCTCCCGAGGGACC
ACAGCCAGCAGCTCTGGGGACGCCCTCGGGAAGGCCTGGCCTCAATCTACTCTCCGGATCACTCAAGCAATAACTTGTGG
TCCAGCCCCTCCACCGCCGTGGGCTCCCCCCAGGGCCTGGGAGGGACGTCGCACTAGCCTGGAGCAGGAGTCCCTGGTGC
CTTATCACCCAGCTACGACGGGGGTCTCCACGGCCTGGAGAGTAAGATAGAAGACCACCTACCTGAACGAGGGCAT

Alignment

ORF - retro_hsap_4123 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.3 %
• Parental protein coverage: 61.75 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MNQPQRMAPVGTDKELSDLLDFSMMFPLPVTNGKGRPASLAGAQFGGSGLEDRPSSGSWGSGDQSSSSFD
          MNQPQRMA.V.TDKELS.L.DFSMMFPLPV.NGKGRPASLAGAQF.GSGLE..PSSGSWGSGDQ.SSSFD
Retrocopy MNQPQRMASVDTDKELSNL-DFSMMFPLPVANGKGRPASLAGAQFRGSGLENWPSSGSWGSGDQNSSSFD

Parental  PSRTFSEGTHFTESHSSLSSSTFLGPGLGGKSGERG-AYASFGRDAGVGGLTQAGFLSGELALNSPGPLS
          PS.TFSEG....ESH.S.S..TFLGPGLGGKS..RG.AY.SFGRDAGV..LTQAGFL.G.LAL.SPGPLS
Retrocopy PSWTFSEGAQLAESHGSHSPFTFLGPGLGGKSS*RG<AYSSFGRDAGVRSLTQAGFLPGKLALSSPGPLS

Parental  PSGMKGTSQYYPSYSGSSR-RRAADGSLDTQPKKVRKVPPGLPSSVYPPSSGEDYGRDATAYPSAKTPSS
          PSGMKGTS.YYPSY..SS..R..AD..LDTQP.KV.KVPPGLPSS.Y.PSSGE.YGRDA.AYPSAKTPSS
Retrocopy PSGMKGTSRYYPSYASSSG<RTEADSGLDTQPTKVGKVPPGLPSSAYLPSSGEEYGRDAAAYPSAKTPSS

Parental  TYPAPFYVADGSLHPSAELWSPPGQAGFGPMLGGGSSPLPLPPGSGPVGSSGSSSTFGGLHQHERMGYQL
          ..PAPFY.ADGSLHP.AELWS..GQ.GFGPMLGGGS.P..LPP.SGPVGS.G.SSTFGGLHQHER.GY.L
Retrocopy ACPAPFYMADGSLHP*AELWSSLGQVGFGPMLGGGSCPSSLPPSSGPVGSGGGSSTFGGLHQHERVGYRL

Parental  HGAEVNGGLPSASSFSSAPGAT-YGGVSSHTPPVSGADSLLGSRGTTAGSSGDALGKA-LASIYSPDHSS
          HG.EVNGGLP.AS.FS.APGAT..GGVSSHT.PV.GAD.LLGSRGTTA.SSGDALGKA.LASIYSPDHSS
Retrocopy HGGEVNGGLPAASTFSLAPGAT<VGGVSSHT-PVGGADNLLGSRGTTASSSGDALGKA<LASIYSPDHSS

Parental  NNFSSSPSTPVGSPQGLAGTSQWPRAGAPGALSPSYDGGLHGLQSKIEDHLDEAIH
          NN..SSPST.VGSPQGL.GTS..P.AG.PGALSPSYDGGLHGL.SKIEDHL.E..H
Retrocopy NNLWSSPSTAVGSPQGLGGTSH*PGAGVPGALSPSYDGGLHGLESKIEDHLPERGH

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	0.02 RPM	23.10 RPM
bodymap2_adrenal	0.10 RPM	47.18 RPM
bodymap2_brain	0.00 RPM	5.88 RPM
bodymap2_breast	0.00 RPM	21.36 RPM
bodymap2_colon	0.00 RPM	25.14 RPM
bodymap2_heart	0.11 RPM	8.20 RPM
bodymap2_kidney	0.04 RPM	14.72 RPM
bodymap2_liver	0.00 RPM	4.96 RPM
bodymap2_lung	0.04 RPM	21.48 RPM
bodymap2_lymph_node	0.00 RPM	76.49 RPM
bodymap2_ovary	0.04 RPM	51.95 RPM
bodymap2_prostate	0.00 RPM	26.05 RPM
bodymap2_skeletal_muscle	0.00 RPM	13.88 RPM
bodymap2_testis	0.08 RPM	141.38 RPM
bodymap2_thyroid	0.00 RPM	24.95 RPM
bodymap2_white_blood_cells	0.00 RPM	35.75 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_4123 was not detected

EST

No EST(s) were mapped for retro_hsap_4123 retrocopy.

TSS

No TSS is located nearby retro_hsap_4123 retrocopy 5' end.

Lab

• Experiment type: PCR amplification
• Forward primer: CTCTCCGGATCACTCAAGCA (20 nt long)
• Reverse primer: GACTCCTGCTCCAGGCTAGT (20 nt long)
• Annealing temperature: 60 °C
• (Expected) product size: 103
• Electrophoresis gel image:
• Additional comment: Black arrows indicate PCR products of retrogenes undergoing deletions in various human populations (A-J). Lane 1 –GeneRuler Low Range DNA Ladder (Thermo Scientific); 2 –Heart; 3 –Brain; 4 –Placenta; 5 –Lung; 6 –Liver; 7 –Skeletal Muscle; 8 –Kidney; 9 –Pancreas; 10 –Spleen; 11 –Thymus; 12 –Prostate; 13 –Testis; 14 –Ovary, 15 –Small intestine 16 –Colon; 17 –Leukocyte; NTC—No template control (water instead of cDNA).

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4123 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2770
Macaca mulatta	retro_mmul_1194

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000071564	1 retrocopy	retro_hsap_4123 ,
Gorilla gorilla	ENSGGOG00000003667	1 retrocopy	retro_ggor_2770,
Macaca mulatta	ENSMMUG00000009017	1 retrocopy	retro_mmul_1194,
Nomascus leucogenys	ENSNLEG00000001742	1 retrocopy	retro_nleu_2472,