RetrogeneDB ID: retro_mdom_1467

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:183471750..183472641(+)
• Located in intron of: ENSMODG00000020564

Retrocopy information

• Ensembl ID: ENSMODG00000020565
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: C11orf54
• Ensembl ID: ENSMODG00000000412
• Aliases: None
• Description: chromosome 11 open reading frame 54 [Source:HGNC Symbol;Acc:30204]

Sequence

>retro_mdom_1467
GTTCTACAGAATGAACTTAAAAATAATTTTGCTGATGTCCAGGTCTCCGTAGTTGATTGCCCTGATCTGTCTAAGGAACC
ATATACATTTCCTGTTAAAGGAATCTGTGGGAAACCGAGAATTGCAGAAGTAGGTGGGGTTCCTTACCTCATGCCTCTTG
TGAATCAAGAAAAGGTTTATGATATGAATACTGTTGCAAAGCAAATTGATCTTCCTGGGGCTTTCATTATTGGAGCAGGA
GAATCCCCATTTCAGACTCTTGGGATCAATGCTGAGTTTAAGCCAATTGTCCAGACTCAAAGTGATCACAAGCCTGCTAT
GAATGGAAGCTACTTTGCCCAGATTAACCCTGCAGATGGAGGGTACCTGCTAGAGAAATATAGTGGGAAATGCAATGACT
TTGGATTTGCCTTACTGGCTAATCTCTTTGCTAGTGAAGGCCAGCCTGGCAAGGTCATTGAAGTAAAAGCCAAAGGAAGA
ACTGGAAAGTACAATTTTGTGACTTGTATGAGACAAACTCTTGAAAAGCATTATGGAGATAAACCTGTAGCGATGGGAGG
AACATTTGTTGTTCAAAAAGGAAAAGTAAAGATTCATATCATGCCCCCAGAATTTTCTTCTTGCCCACTGAACTCTGATG
AGGATGTGAATAATTGGTTGCATTTTTTTGAAATTAAGGCTCCTTTGGTTTGTCAGCCAGTTTTTGTTTCTCGAGACCCG
GGGTTTGATTTACAATTAGAGCATACACACTGTTTTAGTCATCATGGAGAAGGAGGACACTATCATTATGACACCACTCC
AGATACAGTGGAGTATCTTGGGTATTTCCTACCTGCTGAGGTTCTCTATCAAATTGATAAACCAAAGGACACCCATACAT
TTGGGCGAGAT

Alignment

ORF - retro_mdom_1467 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.97 %
• Parental protein coverage: 99.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VLQNGLKNNFADVQVSVVDCPDLSKEPYTFPVKGICGKPRIAEVGGVPYLMPLVNREKVYDMNTVAKQID
          VLQN.LKNNFADVQVSVVDCPDLSKEPYTFPVKGICGKPRIAEVGGVPYLMPLVN.EKVYDMNTVAKQID
Retrocopy VLQNELKNNFADVQVSVVDCPDLSKEPYTFPVKGICGKPRIAEVGGVPYLMPLVNQEKVYDMNTVAKQID

Parental  LPGAFILGAGAAPFQTLGINAEFMPIVQTESDHKPAVNGSYFAQINPADGGYLLEKYSGKYNDFGFALLA
          LPGAFI.GAG..PFQTLGINAEF.PIVQT.SDHKPA.NGSYFAQINPADGGYLLEKYSGK.NDFGFALLA
Retrocopy LPGAFIIGAGESPFQTLGINAEFKPIVQTQSDHKPAMNGSYFAQINPADGGYLLEKYSGKCNDFGFALLA

Parental  NLFASEGQPGKILELVKAKGRTGKYNFVTCMRQTLEKHYGDKPVGMGGTFVVQKGKVKIHIMPPEFSSCP
          NLFASEGQPGK..E.VKAKGRTGKYNFVTCMRQTLEKHYGDKPV.MGGTFVVQKGKVKIHIMPPEFSSCP
Retrocopy NLFASEGQPGKVIE-VKAKGRTGKYNFVTCMRQTLEKHYGDKPVAMGGTFVVQKGKVKIHIMPPEFSSCP

Parental  LNSDEDVNNWLHFFEIKAPLVCQPVFVSRDPGFDLRLEHTHCFSHHGEGGHYHYDTTPDTVEYLGYFLPA
          LNSDEDVNNWLHFFEIKAPLVCQPVFVSRDPGFDL.LEHTHCFSHHGEGGHYHYDTTPDTVEYLGYFLPA
Retrocopy LNSDEDVNNWLHFFEIKAPLVCQPVFVSRDPGFDLQLEHTHCFSHHGEGGHYHYDTTPDTVEYLGYFLPA

Parental  EVLYRIDKPKDTHTFGRD
          EVLY.IDKPKDTHTFGRD
Retrocopy EVLYQIDKPKDTHTFGRD

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	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1467 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1467 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013446	1 retrocopy	retro_chof_593,
Cavia porcellus	ENSCPOG00000014146	1 retrocopy	retro_cpor_1286,
Monodelphis domestica	ENSMODG00000000412	2 retrocopies	retro_mdom_1467 , retro_mdom_852,
Otolemur garnettii	ENSOGAG00000002523	1 retrocopy	retro_ogar_3359,
Tupaia belangeri	ENSTBEG00000007819	1 retrocopy	retro_tbel_4251,
Tursiops truncatus	ENSTTRG00000001140	3 retrocopies	retro_ttru_244, retro_ttru_334, retro_ttru_560,