RetrogeneDB ID: retro_ptro_2851

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 9:95843706..95844294(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TCEA1
• Ensembl ID: ENSPTRG00000020251
• Aliases: None
• Description: None

Sequence

>retro_ptro_2851
AAAGAAAGTAGCTCCAGCGGCAATGTAAGCGGCAGAAAGGATAAGACAAATGCTTGAGATATTTGTTTCATCTGTTCCTT
GGCAAGAAGCGCTTCTGATTCTGTGCGGATGAAGTACAGGGAGATGCTTGCTGCAGCTCTTCGAACAGGAGATGACTGCA
TTGAAATGGGAGCTGATGAGGAAGAATTAGGATCTCGAATTGAGGAAGCTATAGATCCAGAAAGAGGGAATACAGGCATG
AAGTACAAAAATAGAGTCCAAAGTAAGATATCAAATCTTACAGATGCAAAGAATCCAGATTTAAGGAAAAATGCACCGTG
TGGGAATATTCCTCCTGACTTACTTGCTAGAATGACAGCAGAAGAAATGGCTAGTGATGAGCTCAAAGAGATGCAAAAAA
ACTTGACGAAAGAAGCCATCAGAGAGCATCAGATGGCCAAGATAGGTGGAACCCAGCCTGATTCGCTCACATGTGGCAAA
TGTAAAAAGAAGAATTGCACTTCCACACAGGTGCAAGCCTGCAGTGCTGGTGAACCAATGACAACGTTTGTTGACTGTAA
CGAATGTGGAAATCAACAGAAGTTCTGT

Alignment

ORF - retro_ptro_2851 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.27 %
• Parental protein coverage: 65.45 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EESTSSGNVSNRKDETNARD-TYVSSFPRAPSTSDSVRLKCREMLAAALRTGDDYIAIGADEEELGSQIE
          .ES.SSGNVS.RKD.TNA.D.....S..R..S.SDSVR.K.REMLAAALRTGDD.I..GADEEELGS.IE
Retrocopy KESSSSGNVSGRKDKTNA*DICFICSLAR--SASDSVRMKYREMLAAALRTGDDCIEMGADEEELGSRIE

Parental  EAIYQEMRNTDMKYKNRVRSRISNLKDAKNPNLRKNVLCGNIPPDLFARMTAEEMASDELKEMRKNLTKE
          EAI..E..NT.MKYKNRV.S.ISNL.DAKNP.LRKN..CGNIPPDL.ARMTAEEMASDELKEM.KNLTKE
Retrocopy EAIDPERGNTGMKYKNRVQSKISNLTDAKNPDLRKNAPCGNIPPDLLARMTAEEMASDELKEMQKNLTKE

Parental  AIREHQMAKTGGTQTDLFTCGKCKKKNCTYTQVQTRSADEPMTTFVVCNECGNRWKFC
          AIREHQMAK.GGTQ.D..TCGKCKKKNCT.TQVQ..SA.EPMTTFV.CNECGN..KFC
Retrocopy AIREHQMAKIGGTQPDSLTCGKCKKKNCTSTQVQACSAGEPMTTFVDCNECGNQQKFC

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	0.02 RPM	27.69 RPM
SRP007412_cerebellum	0.00 RPM	51.66 RPM
SRP007412_heart	0.00 RPM	32.47 RPM
SRP007412_kidney	0.05 RPM	51.89 RPM
SRP007412_liver	0.00 RPM	63.90 RPM
SRP007412_testis	0.63 RPM	60.91 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2851 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2851 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2851 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001247	1 retrocopy	retro_chof_458,
Callithrix jacchus	ENSCJAG00000014407	1 retrocopy	retro_cjac_2095,
Dasypus novemcinctus	ENSDNOG00000013799	4 retrocopies	retro_dnov_1315, retro_dnov_1853, retro_dnov_839, retro_dnov_952,
Erinaceus europaeus	ENSEEUG00000009220	1 retrocopy	retro_eeur_73,
Homo sapiens	ENSG00000187735	4 retrocopies	retro_hsap_2634, retro_hsap_4159, retro_hsap_4200, retro_hsap_4243,
Gorilla gorilla	ENSGGOG00000023652	3 retrocopies	retro_ggor_2794, retro_ggor_2814, retro_ggor_2844,
Macaca mulatta	ENSMMUG00000016022	1 retrocopy	retro_mmul_1146,
Mus musculus	ENSMUSG00000033813	2 retrocopies	retro_mmus_1369, retro_mmus_3559,
Nomascus leucogenys	ENSNLEG00000000981	3 retrocopies	retro_nleu_1028, retro_nleu_1374, retro_nleu_1384,
Oryctolagus cuniculus	ENSOCUG00000007474	3 retrocopies	retro_ocun_1382, retro_ocun_401, retro_ocun_852,
Pongo abelii	ENSPPYG00000018589	3 retrocopies	retro_pabe_3395, retro_pabe_3436, retro_pabe_3455,
Pan troglodytes	ENSPTRG00000020251	2 retrocopies	retro_ptro_2851 , retro_ptro_2884,
Rattus norvegicus	ENSRNOG00000022323	1 retrocopy	retro_rnor_1089,
Sarcophilus harrisii	ENSSHAG00000013661	1 retrocopy	retro_shar_50,
Ictidomys tridecemlineatus	ENSSTOG00000021179	1 retrocopy	retro_itri_1745,
Tarsius syrichta	ENSTSYG00000001030	1 retrocopy	retro_tsyr_1624,