RetrogeneDB ID: retro_ggor_2814

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 9:79122811..79123399(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TCEA1
• Ensembl ID: ENSGGOG00000023652
• Aliases: None
• Description: None

Sequence

>retro_ggor_2814
AAAGAAAGTAGCTCCAGCGGCAATGTAAGCGGCAGAAAGGATAAGACAAATGCTTGAGATATTTGTTTCATCTGTTCCTT
GGCACGAAGCGCTTCTGATTCTGTGCGGATGAAGTACAGGGAGATGCTTGCTGCAGCTCTTCGAACAGGAGATGACTGCA
TTGAAATGGGAGCTGATCAGGAAGAATTAGGATCTCGAATTGAGGAAGCTGTAGATCCAGAAAGAGGGAATACAGGCATG
AAGTACAAAAATAAAGTCCAAAGTAAGATATCAAATCTTACAGATGCAAAGAATCCAGATTTAAGGAAAAATGCACCGTG
TGGGAATATTCCTCCTGACTTACTTGCTAGAATGACAGCAGAAGAAATGGCTAATGATGAGCTCAAATAGATGCACAAAA
ACTTGACGAAAGAAGCCATCAGAGAGCATCAGATGGCCAAGACAGGTGGAACCCAGCCTGATTTGCTCACATGTGGCAAA
TGTAAAAAGAAGAATTGCACTTCCACACAGGTACAAGCCTGCAGTGCTCGTGAACCAATGACAACGTTTGTTGACTGTAA
CGAATGTGGAAATCAACAGAAGTTCTGT

Alignment

ORF - retro_ggor_2814 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.76 %
• Parental protein coverage: 65.45 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

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

Parental  EAIYQEIRNTDMKYKNRVRSRISNLKDAKNPNLRKNVLCGNIPPDLFARMTAEEMASDELKEMRKNLTKE
          EA...E..NT.MKYKN.V.S.ISNL.DAKNP.LRKN..CGNIPPDL.ARMTAEEMA.DELK.M.KNLTKE
Retrocopy EAVDPERGNTGMKYKNKVQSKISNLTDAKNPDLRKNAPCGNIPPDLLARMTAEEMANDELK*MHKNLTKE

Parental  AIREHQMAKTGGTQTDLFTCGKCKKKNCTYTQVQTRSADEPMTTFVVCNECGNRWKFC
          AIREHQMAKTGGTQ.DL.TCGKCKKKNCT.TQVQ..SA.EPMTTFV.CNECGN..KFC
Retrocopy AIREHQMAKTGGTQPDLLTCGKCKKKNCTSTQVQACSAREPMTTFVDCNECGNQQKFC

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	0.05 RPM	35.77 RPM
SRP007412_cerebellum	0.00 RPM	43.14 RPM
SRP007412_heart	0.00 RPM	8.35 RPM
SRP007412_kidney	0.04 RPM	54.14 RPM
SRP007412_liver	0.00 RPM	58.24 RPM
SRP007412_testis	0.31 RPM	87.85 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_2814 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2814 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,