RetrogeneDB ID: retro_ggor_2312

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 6:6684413..6685108(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CNN3
• Ensembl ID: ENSGGOG00000013870
• Aliases: None
• Description: None

Sequence

>retro_ggor_2312
CAGCTGGGCTTAAAAGAGGGCATCCTCCTCTGTGAACTCATCAACAAGCTGTAGGCAGGCCCAATGAAGAAAGTCAATGA
GTCCTCATTAAACTGGCCTCAGCGGAGAATATTGGCAACTTTATTAAAGCTATTCAGGCTTATGGTGTGAAGCCACGTGA
CATATTTGAAGTAAGTGATCTTTTTAGGATGGAAACATGACCCAAGTTCAGGCTACTCTGGTGGCCCTAGTAGGTTGGCA
AGCACAAAAGGATACAACCATGGACATCAGGGTTAAATATGCAGAAAAACAAACACGACGTTAGGATGAAGGAAAATTAA
AAGCTGCTGAAACTGTAATTGGATTGCAGATGGGAACCAAGGAAGTGCCAGCCAGGCAGGTATGTCAACTTACGGGACTA
CAGGCATCTTTATGATCCCAACATGCAAACTGACAAACGTTTTGACCAGACCACAATTTGTCTGCAGATGGTCACTAACA
AAGCAGACAGCCAGGCAGGGATGTTAGCACCAGGCACCAGAAGGGCCATCTACTATCAGAAGCTAACATTACAGCCAGTA
GACCACTTGACAATTTCTCTACAGATGGGTACCAACAAAGTGGCTTCCCAGAAAAGAATGGGTGTGCATGGGCTTGGGGG
GCAAGTATATGGTCACAAATACTGTGCTGCTCTGACAGAAACTATCATTCACAAC

Alignment

ORF - retro_ggor_2312 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.15 %
• Parental protein coverage: 71.43 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  QLGLKDGIILCELINKLQPGSVKKVNESSLNWPQ-LENIGNFIKAIQAYGMKPHDIFEANDLFE-NGNMT
          QLGLK.GI.LCELINKL..G..KKVNESSLNWPQ..ENIGNFIKAIQAYG.KP.DIFE..DLF...GNMT
Retrocopy QLGLKEGILLCELINKL*AGPMKKVNESSLNWPQ<AENIGNFIKAIQAYGVKPRDIFEVSDLFR<DGNMT

Parental  QVQTTLVALAGLAKTKGFHTTIDIGVKYAEKQTRRFDEGKLKAGQSVIGLQMGTNKC-ASQAGMTAYGTR
          QVQ.TLVAL.G....K...TT.DI.VKYAEKQTRR.DEGKLKA...VIGLQMGT....ASQAGM..YGT.
Retrocopy QVQATLVALVGWQAQKD--TTMDIRVKYAEKQTRR*DEGKLKAAETVIGLQMGTKEV<ASQAGMSTYGTT

Parental  -RHLYDPKMQTDKPFDQTTISLQMGTNKGASQAGMLAPGTRRDIYDQKLTLQPVDNSTISLQMGTNKVAS
          .RHLYDP.MQTDK.FDQTTI.LQM.TNK..SQAGMLAPGTRR.IY.QKLTLQPVD..TISLQMGTNKVAS
Retrocopy <RHLYDPNMQTDKRFDQTTICLQMVTNKADSQAGMLAPGTRRAIYYQKLTLQPVDHLTISLQMGTNKVAS

Parental  QKGMSVYGLGRQVYDPKYCAAPTEPVIHN
          QK.M.V.GLG.QVY..KYCAA.TE..IHN
Retrocopy QKRMGVHGLGGQVYGHKYCAALTETIIHN

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	0.10 RPM	57.50 RPM
SRP007412_cerebellum	0.00 RPM	81.32 RPM
SRP007412_heart	0.00 RPM	16.51 RPM
SRP007412_kidney	0.00 RPM	150.35 RPM
SRP007412_liver	0.00 RPM	85.52 RPM
SRP007412_testis	0.00 RPM	214.66 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_2312 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2312 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3419
Pan troglodytes	retro_ptro_2323

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016707	1 retrocopy	retro_amel_1412,
Bos taurus	ENSBTAG00000020345	1 retrocopy	retro_btau_1211,
Callithrix jacchus	ENSCJAG00000018128	3 retrocopies	retro_cjac_1331, retro_cjac_533, retro_cjac_861,
Echinops telfairi	ENSETEG00000010095	1 retrocopy	retro_etel_638,
Homo sapiens	ENSG00000117519	1 retrocopy	retro_hsap_3419,
Gorilla gorilla	ENSGGOG00000013870	1 retrocopy	retro_ggor_2312 ,
Gorilla gorilla	ENSGGOG00000028153	9 retrocopies	retro_ggor_1199, retro_ggor_1271, retro_ggor_1555, retro_ggor_1612, retro_ggor_1646, retro_ggor_1922, retro_ggor_2370, retro_ggor_305, retro_ggor_762,
Macropus eugenii	ENSMEUG00000002921	2 retrocopies	retro_meug_2020, retro_meug_42,
Macaca mulatta	ENSMMUG00000001690	1 retrocopy	retro_mmul_1747,
Monodelphis domestica	ENSMODG00000004326	1 retrocopy	retro_mdom_442,
Mus musculus	ENSMUSG00000053931	2 retrocopies	retro_mmus_1052, retro_mmus_2544,
Sarcophilus harrisii	ENSSHAG00000002670	1 retrocopy	retro_shar_567,
Vicugna pacos	ENSVPAG00000004889	2 retrocopies	retro_vpac_190, retro_vpac_449,