RetrogeneDB ID: retro_ptro_1581

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2A:25412009..25412740(-)
• Located in intron of: ENSPTRG00000011720

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: SUCLA2
• Ensembl ID: ENSPTRG00000005859
• Aliases: None
• Description: None

Sequence

>retro_ptro_1581
GGTTCAAAAGAAGTTGAGATGAAGGCGCAGGTTTTAGCGGATGGTCGAGGAAAAGGAACATTTGAAAGTGGCCTCAAAGG
AGGAGTGAAGATAGTTTTCTCTCCAGAAGAAGCAAAAGCTGTTTCCTCAGAAATGATTGGGAAAAAGTTGTTTACCAAGC
AAATGGGAGAAAAGGGCGGAATATGCAATCAAGCATTGGAGCGAAAATACCCTAGGGGAGAAGACTACTTTGCAATAGGG
ATGGAAAGGTCATTTCAAGGTCCTGTATTAATAGGAAGTTCACATGGTGGTGTCAACATTGCAGATGTTGCTGCTGAGAC
TCCTGATGCAATTAAAGAACCTGTTGATATTGTAGAAGGCATCAAAAAGGAACAAGCTCTCCGGCTTGAACAGAAGATGG
GATTTCCACCTAATATTGTGGATTCCACAGCAGAAAACATGGTCAAGCTTTACAGCCTTTTTCTGAAATATGATGCAACC
ATGATAAGAAATAAATCCAATGGTGAAGATTCAGACGGAGCTGTGCTGTGATGGATGCAAAGATCAATTTTGACTCTAAT
TCAGCCTATCGCCAAAAGAAAATCTTTGATCTACAGGACTGAACCCAGGAAGATGAAAATGACAAAGACGCTGCTAAGGC
AGATCTCAACTACATTGGCCTGAAAGGAAATACAGACTGTCTAGTAAATGGTGCTGGTTTGGCCATGGCCTCAATGGATA
TAATAAAACTT

Alignment

ORF - retro_ptro_1581 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.8 %
• Parental protein coverage: 53.35 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GSKDVVIKAQVLAGGRGKGTFESGLKGGVKIVFSPEEAKAVSSQMIGKKLFTKQTGEKGRICNQVLVCER
          GSK.V..KAQVLA.GRGKGTFESGLKGGVKIVFSPEEAKAVSS.MIGKKLFTKQ.GEKG.ICNQ.L..ER
Retrocopy GSKEVEMKAQVLADGRGKGTFESGLKGGVKIVFSPEEAKAVSSEMIGKKLFTKQMGEKGGICNQAL--ER

Parental  KYPRREYYFAITMERSFQGPVLIGSSHGGVNIEDVAAETPEAIIKEPIDIEEGIKKEQALQLAQKMGFPP
          KYPR.E.YFAI.MERSFQGPVLIGSSHGGVNI.DVAAETP.AI.KEP.DI.EGIKKEQAL.L.QKMGFPP
Retrocopy KYPRGEDYFAIGMERSFQGPVLIGSSHGGVNIADVAAETPDAI-KEPVDIVEGIKKEQALRLEQKMGFPP

Parental  NIVESAAENMVKLYSLFLKYDATMI-EINPMV-EDSDGAVL-CMDAKINFDSNSAYRQKKIFDLQDWTQE
          NIV.S.AENMVKLYSLFLKYDATMI.EINPMV.EDSDGAVL..MDAKINFDSNSAYRQKKIFDLQD.TQE
Retrocopy NIVDSTAENMVKLYSLFLKYDATMI>EINPMV<EDSDGAVL<VMDAKINFDSNSAYRQKKIFDLQD*TQE

Parental  DERDKDAAKANLNYIGLDGNIGCLVNGAGLAMATMDIIKL
          DE.DKDAAKA.LNYIGL.GN..CLVNGAGLAMA.MDIIKL
Retrocopy DENDKDAAKADLNYIGLKGNTDCLVNGAGLAMASMDIIKL

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	0.46 RPM	52.16 RPM
SRP007412_cerebellum	1.83 RPM	40.80 RPM
SRP007412_heart	5.45 RPM	90.79 RPM
SRP007412_kidney	1.26 RPM	56.54 RPM
SRP007412_liver	0.26 RPM	8.67 RPM
SRP007412_testis	2.21 RPM	19.81 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1581 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1581 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1581 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_1668

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014610	2 retrocopies	retro_acar_26, retro_acar_52,
Callithrix jacchus	ENSCJAG00000009278	2 retrocopies	retro_cjac_1233, retro_cjac_2379,
Cavia porcellus	ENSCPOG00000014961	1 retrocopy	retro_cpor_1113,
Homo sapiens	ENSG00000136143	3 retrocopies	retro_hsap_2236, retro_hsap_2281, retro_hsap_3445,
Gorilla gorilla	ENSGGOG00000008224	3 retrocopies	retro_ggor_1668, retro_ggor_1694, retro_ggor_2327,
Macaca mulatta	ENSMMUG00000007539	1 retrocopy	retro_mmul_1231,
Mustela putorius furo	ENSMPUG00000001488	1 retrocopy	retro_mputfur_768,
Nomascus leucogenys	ENSNLEG00000002948	3 retrocopies	retro_nleu_1963, retro_nleu_2140, retro_nleu_2302,
Otolemur garnettii	ENSOGAG00000007452	1 retrocopy	retro_ogar_2196,
Pongo abelii	ENSPPYG00000005352	2 retrocopies	retro_pabe_1939, retro_pabe_2852,
Pan troglodytes	ENSPTRG00000005859	3 retrocopies	retro_ptro_1581 , retro_ptro_1615, retro_ptro_2337,