RetrogeneDB ID: retro_hsap_73

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 19:57876201..57876624(+)
• Located in intron of: ENSG00000152433

Retrocopy information

• Ensembl ID: ENSG00000256060
• Aliases: TRAPPC2P1, MIP-2A, SEDLP, SEDLP1
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TRAPPC2
• Ensembl ID: ENSG00000196459
• Aliases: TRAPPC2, MIP2A, SEDL, SEDT, TRAPPC2P1, TRS20, ZNF547L, hYP38334
• Description: trafficking protein particle complex 2 [Source:HGNC Symbol;Acc:23068]

Sequence

>retro_hsap_73
ATGTCTGGAAGCTTCTACTTTGTAATTGTTGGTCACCATGATAATCCAGTTTTTGAAATGGAGTTTTTGCCAGCTGGGAA
GGCAGAATCCAAAGACGACCATCGTCATCTGAACCAGTTCATAGCTCATGCTGCTCTCGACCTCGTAGATGAGAACATGT
GGCTGTCGAACAACATGTACTTGAAAACTGTGGACAAGTTCAACGAGTGGTTTGTGTCAGCATTTGTCACCGCGGGGCAT
ATGAGGTTTATTATGCTTCATGACATAAGACAAGAAGATGGAATAAAGAACTTCTTTACTGATGTTTATGATTTATATAT
AAAATTTTCAATGAATCCATTTTATGAACCCAATTCTCCTATTCGATCAAGTGCATTTGACAGAAAAGTTCAGTTTCTTG
GGAAGAAACACCTTTTAAGCTGA

Alignment

ORF - retro_hsap_73 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSGSFYFVIVGHHDNPVFEMEFLPAGKAESKDDHRHLNQFIAHAALDLVDENMWLSNNMYLKTVDKFNEW
          MSGSFYFVIVGHHDNPVFEMEFLPAGKAESKDDHRHLNQFIAHAALDLVDENMWLSNNMYLKTVDKFNEW
Retrocopy MSGSFYFVIVGHHDNPVFEMEFLPAGKAESKDDHRHLNQFIAHAALDLVDENMWLSNNMYLKTVDKFNEW

Parental  FVSAFVTAGHMRFIMLHDIRQEDGIKNFFTDVYDLYIKFSMNPFYEPNSPIRSSAFDRKVQFLGKKHLLS
          FVSAFVTAGHMRFIMLHDIRQEDGIKNFFTDVYDLYIKFSMNPFYEPNSPIRSSAFDRKVQFLGKKHLLS
Retrocopy FVSAFVTAGHMRFIMLHDIRQEDGIKNFFTDVYDLYIKFSMNPFYEPNSPIRSSAFDRKVQFLGKKHLLS

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	4.45 RPM	11.79 RPM
bodymap2_adrenal	4.40 RPM	24.81 RPM
bodymap2_brain	4.76 RPM	19.15 RPM
bodymap2_breast	4.81 RPM	15.78 RPM
bodymap2_colon	2.59 RPM	15.35 RPM
bodymap2_heart	4.87 RPM	5.43 RPM
bodymap2_kidney	2.77 RPM	15.99 RPM
bodymap2_liver	0.89 RPM	5.98 RPM
bodymap2_lung	6.22 RPM	10.18 RPM
bodymap2_lymph_node	4.57 RPM	27.43 RPM
bodymap2_ovary	3.05 RPM	24.66 RPM
bodymap2_prostate	6.55 RPM	22.78 RPM
bodymap2_skeletal_muscle	8.40 RPM	4.93 RPM
bodymap2_testis	9.97 RPM	9.31 RPM
bodymap2_thyroid	4.67 RPM	21.49 RPM
bodymap2_white_blood_cells	3.43 RPM	24.63 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_hsap_73 in 1 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF002CHO	POLR2A	19:57874709..57875207

EST

1 EST(s) were mapped to retro_hsap_73 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BE818730	57876180	57876385	96.6	201	4	196

TSS

No TSS is located nearby retro_hsap_73 retrocopy 5' end.

Lab

retro_hsap_73 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_73 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_72
Macaca mulatta	retro_mmul_326

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000001719	1 retrocopy	retro_acar_53,
Canis familiaris	ENSCAFG00000011754	2 retrocopies	retro_cfam_1608, retro_cfam_368,
Homo sapiens	ENSG00000196459	1 retrocopy	retro_hsap_73 ,
Microcebus murinus	ENSMICG00000004690	1 retrocopy	retro_mmur_1022,
Macaca mulatta	ENSMMUG00000022619	1 retrocopy	retro_mmul_326,
Monodelphis domestica	ENSMODG00000017312	2 retrocopies	retro_mdom_1737, retro_mdom_1901,
Mus musculus	ENSMUSG00000079317	2 retrocopies	retro_mmus_198, retro_mmus_2522,
Otolemur garnettii	ENSOGAG00000002870	2 retrocopies	retro_ogar_369, retro_ogar_60,
Pan troglodytes	ENSPTRG00000021674	1 retrocopy	retro_ptro_72,
Sorex araneus	ENSSARG00000006353	1 retrocopy	retro_sara_244,
Ictidomys tridecemlineatus	ENSSTOG00000025097	1 retrocopy	retro_itri_1014,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	5.44 RPM
CEU_NA11843	5.23 RPM
CEU_NA11930	3.39 RPM
CEU_NA12004	4.94 RPM
CEU_NA12400	6.21 RPM
CEU_NA12751	4.03 RPM
CEU_NA12760	3.91 RPM
CEU_NA12827	6.04 RPM
CEU_NA12872	4.25 RPM
CEU_NA12873	3.54 RPM
FIN_HG00183	5.08 RPM
FIN_HG00277	4.92 RPM
FIN_HG00315	5.52 RPM
FIN_HG00321	4.11 RPM
FIN_HG00328	4.21 RPM
FIN_HG00338	4.90 RPM
FIN_HG00349	5.38 RPM
FIN_HG00375	6.09 RPM
FIN_HG00377	5.67 RPM
FIN_HG00378	4.82 RPM
GBR_HG00099	4.74 RPM
GBR_HG00111	4.92 RPM
GBR_HG00114	4.73 RPM
GBR_HG00119	4.26 RPM
GBR_HG00131	5.58 RPM
GBR_HG00133	5.67 RPM
GBR_HG00134	4.41 RPM
GBR_HG00137	6.08 RPM
GBR_HG00142	5.28 RPM
GBR_HG00143	4.37 RPM
TSI_NA20512	5.17 RPM
TSI_NA20513	3.65 RPM
TSI_NA20518	4.88 RPM
TSI_NA20532	3.78 RPM
TSI_NA20538	3.87 RPM
TSI_NA20756	6.37 RPM
TSI_NA20765	3.73 RPM
TSI_NA20771	5.56 RPM
TSI_NA20786	5.57 RPM
TSI_NA20798	5.46 RPM
YRI_NA18870	6.26 RPM
YRI_NA18907	4.44 RPM
YRI_NA18916	4.50 RPM
YRI_NA19093	4.58 RPM
YRI_NA19099	5.49 RPM
YRI_NA19114	4.38 RPM
YRI_NA19118	3.77 RPM
YRI_NA19213	5.19 RPM
YRI_NA19214	4.55 RPM
YRI_NA19223	3.82 RPM

---

Indel association:

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