RetrogeneDB ID: retro_ggor_984

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 13:19031679..19032684(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000000169
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CSNK1A1
• Ensembl ID: ENSGGOG00000013926
• Aliases: None
• Description: None

Sequence

>retro_ggor_984
ATGGCAAACAACAGCGGCTCCAAAGCCGAACTCGTTGTGGGAGGGAAATACAAACTGGTGCGGAAGATCGGGTCTGGCTC
CTTTGGAGACGTTTATCTGGGCATCACCACCACCAACGGCGAGGAAGTAGCAGTGAAACTGGAATCTCAGAAGGTCAAGC
ACCCCCAGTTGCTGTATGAGAGAAAACTCTACACGATTCTTCAAGGTGGGGTTGGCATCCCCCACATGCACTGGTATGGT
CAGGAAAAAGACAACAATGTGCTAGTCATGGACCTTCTGGGACCCAGCCTCGAAGACCTCTTTAATTTCTGTTCAAGAAG
GTTCACCATGAAAACTGTACTTATGTTAGCCGACCAGATGATCAGCAGAATTGAATACGTGCATACAAAGAATTTTCTAC
ACCGAGACATTAAACCAGATAACTTCCTGATGGGTACTGGGCGTCACTGTAATAAGTTGTTCCTTATTGATTTTGGTTTG
GCCAAAAAGTACAGAGACAACAGGACCAGGCAACACATACCGTACAGAGAAGATAAACACCTCATTGGCACTGTCCGATA
TGCCAGCATCAATGCACATCTTGGTATTGAGCAGAGCCGCCGAGATGACATGGAATCCTTAGGCTACGTTTTCATGTATT
TTAATAGAACCAGCCTGCCGTGGCAAGGACTAAGGGCTATGACAAAAAAACAAAAATATGAAAAGATCAGTGAGAAGAAG
ATGTCCACCCCTGTTGAAGTTTTATGTAAGGGGTTTCCTGCAGAATTCGCCATGTACTTGAACTACTGTCGTGGGCTGCG
CTTTGAGGAAGTCCCAGATTACATGTATCTGAGGCAGCTATTCCGCATTCTTTTCAGGACCCTGAACCACCAATATGACT
ACACATTTGATTGGACGATGTTAAAGCAGAAAGCAGCACAGCAGGCAGCCTCTTCCAGTGGGCAGGGTCAGCAGGCCCAA
ACCCAGACAGGCAAGCAAACTGAAAAAAACAAGAATAATGTGAAA

Alignment

ORF - retro_ggor_984 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.85 %
• Parental protein coverage: 99.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASSSGSKAEFIVGGKYKLVRKIGSGSFGDIYLAINITNGEEVAVKLESQKARHPQLLYESKLYKILQGG
          MA..SGSKAE..VGGKYKLVRKIGSGSFGD.YL.I..TNGEEVAVKLESQK..HPQLLYE.KLY.ILQGG
Retrocopy MANNSGSKAELVVGGKYKLVRKIGSGSFGDVYLGITTTNGEEVAVKLESQKVKHPQLLYERKLYTILQGG

Parental  VGIPHIRWYGQEKDYNVLVMDLLGPSLEDLFNFCSRRFTMKTVLMLADQMISRIEYVHTKNFIHRDIKPD
          VGIPH..WYGQEKD.NVLVMDLLGPSLEDLFNFCSRRFTMKTVLMLADQMISRIEYVHTKNF.HRDIKPD
Retrocopy VGIPHMHWYGQEKDNNVLVMDLLGPSLEDLFNFCSRRFTMKTVLMLADQMISRIEYVHTKNFLHRDIKPD

Parental  NFLMGIGRHCNKLFLIDFGLAKKYRDNRTRQHIPYREDKNLTGTARYASINAHLGIEQSRRDDMESLGYV
          NFLMG.GRHCNKLFLIDFGLAKKYRDNRTRQHIPYREDK.L.GT.RYASINAHLGIEQSRRDDMESLGYV
Retrocopy NFLMGTGRHCNKLFLIDFGLAKKYRDNRTRQHIPYREDKHLIGTVRYASINAHLGIEQSRRDDMESLGYV

Parental  LMYFNRTSLPWQGLKAATKKQKYEKISEKKMSTPVEVLCKGFPAEFAMYLNYCRGLRFEEAPDYMYLRQL
          .MYFNRTSLPWQGL.A......YEKISEKKMSTPVEVLCKGFPAEFAMYLNYCRGLRFEE.PDYMYLRQL
Retrocopy FMYFNRTSLPWQGLRAMXXXXXYEKISEKKMSTPVEVLCKGFPAEFAMYLNYCRGLRFEEVPDYMYLRQL

Parental  FRILFRTLNHQYDYTFDWTMLKQKAAQQAASSSGQGQQAQTPTGKQTDKTKSNMK
          FRILFRTLNHQYDYTFDWTMLKQKAAQQAASSSGQGQQAQT.TGKQT.K.K.N.K
Retrocopy FRILFRTLNHQYDYTFDWTMLKQKAAQQAASSSGQGQQAQTQTGKQTEKNKNNVK

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	0.00 RPM	39.61 RPM
SRP007412_cerebellum	0.00 RPM	41.84 RPM
SRP007412_heart	0.03 RPM	12.66 RPM
SRP007412_kidney	0.04 RPM	37.37 RPM
SRP007412_liver	0.18 RPM	27.83 RPM
SRP007412_testis	13.26 RPM	89.82 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_984 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_984 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_32
Pan troglodytes	retro_ptro_7
Pongo abelii	retro_pabe_170
Macaca mulatta	retro_mmul_295
Callithrix jacchus	retro_cjac_2680

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005326	2 retrocopies	retro_btau_1662, retro_btau_49,
Canis familiaris	ENSCAFG00000018286	1 retrocopy	retro_cfam_1887,
Callithrix jacchus	ENSCJAG00000021121	1 retrocopy	retro_cjac_2680,
Homo sapiens	ENSG00000113712	1 retrocopy	retro_hsap_32,
Gorilla gorilla	ENSGGOG00000013926	3 retrocopies	retro_ggor_1178, retro_ggor_742, retro_ggor_984 ,
Myotis lucifugus	ENSMLUG00000002910	4 retrocopies	retro_mluc_1531, retro_mluc_2134, retro_mluc_2215, retro_mluc_597,
Macaca mulatta	ENSMMUG00000001758	2 retrocopies	retro_mmul_2207, retro_mmul_295,
Monodelphis domestica	ENSMODG00000009937	1 retrocopy	retro_mdom_2005,
Oryctolagus cuniculus	ENSOCUG00000006669	7 retrocopies	retro_ocun_1068, retro_ocun_1098, retro_ocun_1506, retro_ocun_500, retro_ocun_502, retro_ocun_506, retro_ocun_644,
Otolemur garnettii	ENSOGAG00000003253	2 retrocopies	retro_ogar_1195, retro_ogar_825,
Sorex araneus	ENSSARG00000011446	1 retrocopy	retro_sara_518,
Sarcophilus harrisii	ENSSHAG00000015356	1 retrocopy	retro_shar_834,
Sus scrofa	ENSSSCG00000014435	1 retrocopy	retro_sscr_560,
Ictidomys tridecemlineatus	ENSSTOG00000022141	1 retrocopy	retro_itri_1378,
Drosophila melanogaster	FBgn0015024	4 retrocopies	retro_dmel_10, retro_dmel_32, retro_dmel_40, retro_dmel_67,