RetrogeneDB ID: retro_mdom_2005

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: X:65905480..65906553(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000009077
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CSNK1A1
• Ensembl ID: ENSMODG00000009937
• Aliases: None
• Description: casein kinase 1, alpha 1 [Source:HGNC Symbol;Acc:2451]

Sequence

>retro_mdom_2005
TCCGAGTTTATTGTTGGAGGAAAATATAAATTGATCAGGAAAATTGGGGCCGGCTCCTTTGGAGATATCTATCTGGCCAT
CAATATCACCAATAATGAAGAATTGGCTGTGAAGCTAGAATCTCAGAAGGCCAGACACCCACAGCTGCTGTATGAAAGCC
GGCTCTATAAGCTTCTTCAGGGTGGGATGGGCATTCCCCGAACCCGCTGGTATGGTCAGGAGAAAGAATACAATATCCTT
GTCATGGATCTACTTGGGCCTAGTCTTGAAGACCTCTTCAATTTCTGTTCCCGTAAATTCACGTTGAAAACCGTCCTGAT
GTTGGCTGACCAGATGATTAGCAGAATTGAATATGTTCATACAAAGAACTTTATTCACAGAGACATTAAACCAGATAATT
TTCTGATGGGTATTGGGCGCCCTCGAAATAGGGCTGCTGGATCTGCAGCAGGAAAGAGAAAAAGAGGCGGGGCAGCTGCC
AATCGGGCTCAGGACCCATCTTTTTCAGGATTAAACCAGTTATTCCTTATTGACTTTGGTTTGGCTAAACGCTACCGAGA
CAACAGAACGAAGCAACACATACCCTACCGAGAAGATAAAAATTTCACTGGCACTGCCCGGTATGCCAGCATCAATGCAC
ACCTGGGCATTGAGCAGAGCCGTAGAGATGATGTAGAGTCCTTGGGCTATGTCTTGATGTATTTCAACAGGAGCAGCCTG
CCCTGGCAAGGAATAAAGGCGGCAACCAAGAAGCAAAAGTATGAAAAAATTATTGAAAAGAAGATGTCCATCCCTGTTGA
TATTCTGTGTCAGGGGTTTCCAACAGAATTTGCCATGTATCTCAACTACTGCCGTGGCCTTCGCTTTGAAGAAGCACCCG
ATTACATGTACCTGAGGCAGCTATTTCGCATCCTCTTCAGGAGCCTGAGCTACAAGTACGACTTCATGTTTGATTGGACA
CTGCTGAAGCAGAAAGCAGAGCAGGAGCAGGCAGCCTCGTCCTCGGAGCAGGGACCGCAGACCCAGCCCCCTCCACCACC
TAAACAGACCAAACCAAGAAGAGTAACCAGAAG

Alignment

ORF - retro_mdom_2005 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.89 %
• Parental protein coverage: 97.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NEFIVGGKYKLVRKIGSGSFGDIYLAINVTNGEEVAVKLESQKARHPQLLYESKLYKILQGGVGIPHIRW
          .EFIVGGKYKL.RKIG.GSFGDIYLAIN.TN.EE.AVKLESQKARHPQLLYES.LYK.LQGG.GIP..RW
Retrocopy SEFIVGGKYKLIRKIGAGSFGDIYLAINITNNEELAVKLESQKARHPQLLYESRLYKLLQGGMGIPRTRW

Parental  YGQEKDYNVLVMDLLGPSLEDLFNFCSRRFTMKTVLMLADQMISRIEFVHTKNFIHRDIKPDNFLMGIGR
          YGQEK.YN.LVMDLLGPSLEDLFNFCSR.FT.KTVLMLADQMISRIE.VHTKNFIHRDIKPDNFLMGIGR
Retrocopy YGQEKEYNILVMDLLGPSLEDLFNFCSRKFTLKTVLMLADQMISRIEYVHTKNFIHRDIKPDNFLMGIGR

Parental  HCNKCLESPVGKRKRS-MTVSTSQDPSFSGLNQLFLIDFGLAKKYRDNRTRQHIPYREDKNLTGTARYAS
          ..N....S..GKRKR........QDPSFSGLNQLFLIDFGLAK.YRDNRT.QHIPYREDKN.TGTARYAS
Retrocopy PRNRAAGSAAGKRKRGGAAANRAQDPSFSGLNQLFLIDFGLAKRYRDNRTKQHIPYREDKNFTGTARYAS

Parental  INAHLGIEQSRRDDMESLGYVLMYFNRTSLPWQGLKAATKKQKYEKISEKKMSTPVEVLCKGFPAEFAMY
          INAHLGIEQSRRDD.ESLGYVLMYFNR.SLPWQG.KAATKKQKYEKI.EKKMS.PV..LC.GFP.EFAMY
Retrocopy INAHLGIEQSRRDDVESLGYVLMYFNRSSLPWQGIKAATKKQKYEKIIEKKMSIPVDILCQGFPTEFAMY

Parental  LNYCRGLRFEEAPDYMYLRQLFRILFRTLNHQYDYTFDWTMLKQKAAQ-QAASSSGQGQQAQTPTGKQ-T
          LNYCRGLRFEEAPDYMYLRQLFRILFR.L...YD..FDWT.LKQKA.Q.QAASSS.QG.Q.Q.P.....T
Retrocopy LNYCRGLRFEEAPDYMYLRQLFRILFRSLSYKYDFMFDWTLLKQKAEQEQAASSSEQGPQTQPPPPPK<T

Parental  DKT-KSNMK
          D.T.KSN.K
Retrocopy DQTKKSNQK

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	0.00 RPM	456.52 RPM
SRP007412_cerebellum	0.00 RPM	514.49 RPM
SRP007412_heart	0.00 RPM	274.91 RPM
SRP007412_kidney	0.00 RPM	297.60 RPM
SRP007412_liver	0.00 RPM	197.37 RPM
SRP007412_testis	0.00 RPM	176.79 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_2005 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_2005 was not experimentally validated.

Homology

Retrocopy orthology:

Monodelphis domestica does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 30 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,
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,