RetrogeneDB ID: retro_ptro_1525

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 22:49686372..49687135(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000029388
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SNRPA1
• Ensembl ID: ENSPTRG00000007513
• Aliases: None
• Description: None

Sequence

>retro_ptro_1525
ATGGTCAAGCTGACGGCGGAGCTGATCGAGCAGGCGGCGCAGTACACCAACGCGGTGCGCGACCGGGAGCTGGACCTCCG
GGGGTATACAATTCCCGTCATTGAAAATCTAGGTGCTACATTAGACCAGTTTGATGCTATTGATTTTTCTGACAATGAGA
TCAGGAAACTGGATGGTTTTCCTTTGTTGAGAAGACTGAAAACGTTGTTAGTGAACAAAACAGAATATGCCGTATAGGTG
AGGGACTTGATCAGGCTCTGCCCTGTCTGACAGAACTCATTCTCACCAATAATAGGCTCATGGAACTGGGTGATCTGGAC
CCTCTGGCATCTCTCAAATCGCTGACTTACCTAAGTATCCTAAGAAATCCAGTAACCAATAAGAAGCATTACAGATTGTA
TGTGATTTATAAAGTTCCGCAAGTCAGAGTACTGGATTTCCAGAAAGTGAAACTAAAGAGCGTCAGGAAGCAGAGAAAAT
GTTCAAGGGCAAACGGGGTGCACAGCTTGCAAAGGATATTGCCAGGAGAAGCAACACTTTTAATCCAGGTGCTGGTTTGC
CAACTGACAAAAAGAAAGGTGGGCCATCTCCAGGGGATGTAGAAGCAATCAAGAATGCTATAGCAAATGCTTCAACTCTG
GCTGAAGTGGAGAGGCTGAAGGGGTTGCTGCAGTCTGGTCAGATCCCTGGCAGAGAACGCAGATTGGGGCCCACTGATGA
TGGTGAAGAAGAGATGGAAGAAGACACAGTCACAAACGGGTCC

Alignment

ORF - retro_ptro_1525 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.89 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MVKLTAELIEQAAQYTNAVRDRELDLRGYKIPVIENLGATLDQFDAIDFSDNEIRKLDGFPLLRRLKTLL
          MVKLTAELIEQAAQYTNAVRDRELDLRGY.IPVIENLGATLDQFDAIDFSDNEIRKLDGFPLLRRLKTLL
Retrocopy MVKLTAELIEQAAQYTNAVRDRELDLRGYTIPVIENLGATLDQFDAIDFSDNEIRKLDGFPLLRRLKTLL

Parental  VNN-NRICRIGEGLDQALPCLTELILTNNSLVELGDLDPLASLKSLTYLSILRNPVTNKKHYRLYVIYKV
          VN..NRICRIGEGLDQALPCLTELILTNN.L.ELGDLDPLASLKSLTYLSILRNPVTNKKHYRLYVIYKV
Retrocopy VNK<NRICRIGEGLDQALPCLTELILTNNRLMELGDLDPLASLKSLTYLSILRNPVTNKKHYRLYVIYKV

Parental  PQVRVLDFQKVKLK-ERQEAEKMFKGKRGAQLAKDIARRSKTFNPGAGLPTDKKKGGPSPGDVEAIKNAI
          PQVRVLDFQKVKLK.ERQEAEKMFKGKRGAQLAKDIARRS.TFNPGAGLPTDKKKGGPSPGDVEAIKNAI
Retrocopy PQVRVLDFQKVKLK<ERQEAEKMFKGKRGAQLAKDIARRSNTFNPGAGLPTDKKKGGPSPGDVEAIKNAI

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
SRP007412_brain_prefrontal_cortex	0.38 RPM	16.73 RPM
SRP007412_cerebellum	0.57 RPM	27.78 RPM
SRP007412_heart	0.38 RPM	12.71 RPM
SRP007412_kidney	0.29 RPM	19.06 RPM
SRP007412_liver	0.43 RPM	18.13 RPM
SRP007412_testis	0.11 RPM	34.04 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1525 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1525 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1525 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2148
Homo sapiens	retro_hsap_2601

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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,