RetrogeneDB ID: retro_hsap_2601

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 22:51193098..51193861(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000213683
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SNRPA1
• Ensembl ID: ENSG00000131876
• Aliases: SNRPA1, Lea1
• Description: small nuclear ribonucleoprotein polypeptide A' [Source:HGNC Symbol;Acc:11152]

Sequence

>retro_hsap_2601
ATGGTCAAGCTGACGGCGGAGCTGATCGAGCAGGCGGCGCAGTACACCAGCGCGGTGCGCGACCGGGAGCTGGACCTCCG
GGGGTATAAAATTCCCGTCATTGAAAATCTAGGTGCTACGTTAGACCAGTTTGATGCTATTGATTTTTCTGACAATGAGA
TCAGGAAACTGGATGGTTTTCCTTTGTTGAGAAGACTGAAAACGTTGTTAGTGAACAAAACAGAATATGCCGTATAGGTG
AGGGACTTGATCAGGCTCTGCCCTGTCTGACAGAACTCATTCTCACCAATAATAGGCTCGTGGAACTGGGTGATCTGGAC
CCTCTGGCATCTCTCAAATCGCTGACTTACCTAAGTATCCTAAGAAATCCAGTAACCAATAAGAAGCATTACAGATTGTA
TGTGATTTATAAAGTTCCGCAAATCAGAGTACTGGATTTCCAGAAAGTGAAACTAAAGAGCGTCAGGAAGCAGAGAAAAT
GTTCAAGGGCAAACGGGGTGCACAGCTTGCAAAGGATATTGCCAGGAGAAGCAAAACTTTTAATCCAGGTGCTGGTTTGC
CAACTGACAAAAAGAAAGGTGGGCCATCTCCAGGGGATGTAGAAGCAATCAAGAATGCTATAGCAAATGCTTCAACTCTG
GCTGAAGTGGAGAGGCTGAAGGGGTTGCTGCAGTCTGGTCAGATCCCTGGCAGAGAACGCAGATTGGGGCCCACTGATGA
TGGTGAAGAAGAGATGGAAGAAGACACAGTCACAAACGGGTCC

Alignment

ORF - retro_hsap_2601 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.28 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MVKLTAELIEQAAQYTNAVRDRELDLRGYKIPVIENLGATLDQFDAIDFSDNEIRKLDGFPLLRRLKTLL
          MVKLTAELIEQAAQYT.AVRDRELDLRGYKIPVIENLGATLDQFDAIDFSDNEIRKLDGFPLLRRLKTLL
Retrocopy MVKLTAELIEQAAQYTSAVRDRELDLRGYKIPVIENLGATLDQFDAIDFSDNEIRKLDGFPLLRRLKTLL

Parental  VNN-NRICRIGEGLDQALPCLTELILTNNSLVELGDLDPLASLKSLTYLSILRNPVTNKKHYRLYVIYKV
          VN..NRICRIGEGLDQALPCLTELILTNN.LVELGDLDPLASLKSLTYLSILRNPVTNKKHYRLYVIYKV
Retrocopy VNK<NRICRIGEGLDQALPCLTELILTNNRLVELGDLDPLASLKSLTYLSILRNPVTNKKHYRLYVIYKV

Parental  PQVRVLDFQKVKL-KERQEAEKMFKGKRGAQLAKDIARRSKTFNPGAGLPTDKKKGGPSPGDVEAIKNAI
          PQ.RVLDFQKVKL.KERQEAEKMFKGKRGAQLAKDIARRSKTFNPGAGLPTDKKKGGPSPGDVEAIKNAI
Retrocopy PQIRVLDFQKVKL<KERQEAEKMFKGKRGAQLAKDIARRSKTFNPGAGLPTDKKKGGPSPGDVEAIKNAI

Parental  ANASTLAEVERLKGLLQSGQIPGRERRSGPTDDGEEEMEEDTVTNGS
          ANASTLAEVERLKGLLQSGQIPGRERR.GPTDDGEEEMEEDTVTNGS
Retrocopy ANASTLAEVERLKGLLQSGQIPGRERRLGPTDDGEEEMEEDTVTNGS

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	16.38 RPM
bodymap2_adrenal	0.10 RPM	71.25 RPM
bodymap2_brain	0.05 RPM	22.17 RPM
bodymap2_breast	0.04 RPM	17.37 RPM
bodymap2_colon	0.04 RPM	16.01 RPM
bodymap2_heart	0.00 RPM	12.44 RPM
bodymap2_kidney	0.00 RPM	17.66 RPM
bodymap2_liver	0.02 RPM	16.05 RPM
bodymap2_lung	0.00 RPM	28.80 RPM
bodymap2_lymph_node	0.00 RPM	23.83 RPM
bodymap2_ovary	0.04 RPM	25.48 RPM
bodymap2_prostate	0.00 RPM	22.41 RPM
bodymap2_skeletal_muscle	0.00 RPM	7.58 RPM
bodymap2_testis	0.15 RPM	33.43 RPM
bodymap2_thyroid	0.04 RPM	40.64 RPM
bodymap2_white_blood_cells	0.00 RPM	12.42 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2601 was not detected

EST

No EST(s) were mapped for retro_hsap_2601 retrocopy.

TSS

No TSS is located nearby retro_hsap_2601 retrocopy 5' end.

Lab

retro_hsap_2601 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2601 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2148
Pan troglodytes	retro_ptro_1525

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007128	1 retrocopy	retro_amel_850,
Bos taurus	ENSBTAG00000013593	1 retrocopy	retro_btau_1453,
Canis familiaris	ENSCAFG00000010564	1 retrocopy	retro_cfam_1208,
Echinops telfairi	ENSETEG00000010019	1 retrocopy	retro_etel_1366,
Felis catus	ENSFCAG00000018594	1 retrocopy	retro_fcat_322,
Homo sapiens	ENSG00000131876	2 retrocopies	retro_hsap_2148, retro_hsap_2601 ,
Loxodonta africana	ENSLAFG00000012638	1 retrocopy	retro_lafr_1230,
Myotis lucifugus	ENSMLUG00000014213	1 retrocopy	retro_mluc_2442,
Mustela putorius furo	ENSMPUG00000010938	1 retrocopy	retro_mputfur_1139,
Oryctolagus cuniculus	ENSOCUG00000017417	3 retrocopies	retro_ocun_1248, retro_ocun_1775, retro_ocun_366,
Pan troglodytes	ENSPTRG00000007513	1 retrocopy	retro_ptro_1525,
Tupaia belangeri	ENSTBEG00000001669	2 retrocopies	retro_tbel_1772, retro_tbel_3447,
Tarsius syrichta	ENSTSYG00000003965	2 retrocopies	retro_tsyr_1229, retro_tsyr_1943,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.06 RPM
CEU_NA11843	0.06 RPM
CEU_NA11930	0.26 RPM
CEU_NA12004	0.04 RPM
CEU_NA12400	0.04 RPM
CEU_NA12751	0.02 RPM
CEU_NA12760	0.04 RPM
CEU_NA12827	0.05 RPM
CEU_NA12872	0.03 RPM
CEU_NA12873	0.03 RPM
FIN_HG00183	0.22 RPM
FIN_HG00277	0.07 RPM
FIN_HG00315	0.08 RPM
FIN_HG00321	0.09 RPM
FIN_HG00328	0.05 RPM
FIN_HG00338	0.04 RPM
FIN_HG00349	0.06 RPM
FIN_HG00375	0.05 RPM
FIN_HG00377	0.05 RPM
FIN_HG00378	0.08 RPM
GBR_HG00099	0.15 RPM
GBR_HG00111	0.02 RPM
GBR_HG00114	0.13 RPM
GBR_HG00119	0.07 RPM
GBR_HG00131	0.03 RPM
GBR_HG00133	0.07 RPM
GBR_HG00134	0.09 RPM
GBR_HG00137	0.08 RPM
GBR_HG00142	0.17 RPM
GBR_HG00143	0.06 RPM
TSI_NA20512	0.08 RPM
TSI_NA20513	0.05 RPM
TSI_NA20518	0.11 RPM
TSI_NA20532	0.17 RPM
TSI_NA20538	0.09 RPM
TSI_NA20756	0.20 RPM
TSI_NA20765	0.06 RPM
TSI_NA20771	0.06 RPM
TSI_NA20786	0.05 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.17 RPM
YRI_NA18907	0.07 RPM
YRI_NA18916	0.02 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.05 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.08 RPM
YRI_NA19213	0.10 RPM
YRI_NA19214	0.05 RPM
YRI_NA19223	0.02 RPM

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Indel association:

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