RetrogeneDB ID: retro_mdom_110

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:484697551..484699414(-)
• Located in intron of: ENSMODG00000016550

Retrocopy information

• Ensembl ID: ENSMODG00000023258
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000020527
• Aliases: None
• Description: None

Sequence

>retro_mdom_110
GAGGCGGCAGCGGCTGCGGCAGCTATGTCCGTGGCGGCGGGGGATGGTCCGGGCGGGGACTCGCGGTTGGACCAGGCGGC
CACCCAGTGGTTGCGGTGGGACAAGAATCCTAAAACTTTAGAAATGGTGAAACAAATAATTGCCAATAACAATAGAGTAG
AACTACAAAAATGTTTTGGTTCCCGAATGGAGTTTGGAACTGCTGGCCTTCGAGCTGCAATGGGACCTGGATTTGCACAG
ATGAATGACTTAACTATTATTCAGACTACTCAGGGATTATGCAGATATTTGGAAAAAACATTCAGTGATCTAAAGAAAAG
AGGTGTGGTGATTGGCTATGATGCCCGGGCTCACCCATCCAGTGGAGGTGGCAGCAAAAGGTTTGCACAGCTAGCCGCAA
CAGCTTTTATTAGTCAGGGGGTTCCTGTGTATCTCTTTTCTAATATAACACCAACTCCCTTTGTGCCCTATACCGTCTCC
CATCTGAATCTTTGTGCAGGAATCATGGTCACAGCCTCCCACAACCCAAAGCAGGATAATGGTTATAAGGTCTATTGGGA
TAATGGAGCTCAGATCATTTCTCCTCATGACAAAGGAATTTCTCAAGCTATTGAAGAAAATCTGGAGCCATGGACTAAGG
CATGGGATGACAGTATAATTAATAACAACCCACTTCATCATGATCCATACTCTACAATCAATAATGATTACTTTGAAGAC
CTAAAGAAATACTGTTTTCACAGAAATATCGACCAGTCAACCCAATTGAAATTTGTCCATACTTCTGTTCATGGAGTAGG
CCATGACTTTGTACAGTCTGCTTTCAAGGCATTTGACTTTGTTCCTCCCGATGCTGTTCCTGAACAGAAAGCTCCTGACC
CAGAATTTCCAACAGTGAAATACCCAAATCCTGAAGAGGGTAAAGGTGTCTTGACATTATCATTTGCTTTGGCTGAAAAA
ACACAGGCTAAAATCATTTTAGCAAATGATCCAGATGCTGATAGACTTGCAGTAGCAGAACAGCAAGAAAATGGTGAATG
GAAAGTGTTTTCTGGAAATGAGATGGGTGCTCTTTTAGGTTGGTGGCTCTTTACCTGTTGGAAGGAAAAGAATCAAGATC
AAAATGCTCTTAAAGACCTATACATGTTATCCAGCACAGTTTCTTCAAAGATCCTGAGGGCCATTGCCTTGAAGGAAGGT
TTTCATTTTGAGGAAACGTTAACTGGCTTTAAGTGGATGGGAAATCGAGCAAAACAATTAATAGACCAGGGAAAAACTGT
TCTTTTTGCATTTGAAGAAGCTATTGGCTATATGTGCTGTCCTTTTGTTCTGGACAAAGATGGTGTCAGTGCTGCTGTTA
TAAGTGCAGAATTGGCTAGTTTTCTAGCAACTAAGAATATGTCTTTGGCTCAGCAACTAAAAGCCATCTATGTTGAATAT
GGCTACCATATCACCAAGGCATCATACTTTATTTGCCATGACCAAAACATCATCCAAAACTTATTTGAAAATCTTAGAAA
TTATGATGGGAAGAACAATTACCCAAAGACTTGTGGCAAATTTGAAGTTTCTGGAATTAGGGATCTTACCACTGGCTATG
ATAGCAGCCAACCTGACAAAAAAGCTATTCTTCCTACGAGTAAAAGCAGCCAAATGATTACTTTTACCTTTGCAAATGGA
GGAGTGGCAACTCTAAGGACCAGTGGAACAGAACCCAAAATCAAATATTATGCTGAACTCTGTGTGCCTCCTGGAAACAG
TGATCATGAACAGCTAAAGAAAGAATTGGATGAACTCGTCAGTGCCATTGAAGAATATTTCTTTGAGCCAGAAAAAAACA
AGCTACAGCCTAAGTCAGAGTAA

Alignment

ORF - retro_mdom_110 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.52 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EAAAAAAAMSVAAGDGPGGDSRLDQAATQWLRWDKNPKTLEMVKQIIANNNRVELQKCFGSRMEFGTAGL
          EAAAAAAAMSVAAGDGPGGDSRLDQAATQWLRWDKNPKTLEMVKQIIANNNRVELQKCFGSRMEFGTAGL
Retrocopy EAAAAAAAMSVAAGDGPGGDSRLDQAATQWLRWDKNPKTLEMVKQIIANNNRVELQKCFGSRMEFGTAGL

Parental  RAAMGPGFAQMNDLTIIQTTQQLSCEYLEKTFSDLKKRGVVIGYDARAHPSSGGGSKRFAQLAATAFISQ
          RAAMGPGFAQMNDLTIIQTTQ.L.C.YLEKTFSDLKKRGVVIGYDARAHPSSGGGSKRFAQLAATAFISQ
Retrocopy RAAMGPGFAQMNDLTIIQTTQGL-CRYLEKTFSDLKKRGVVIGYDARAHPSSGGGSKRFAQLAATAFISQ

Parental  GVPVYLFSNITPTPFVPYTVSHLNLCAGIMVTASHNPKQDNGYKVYWDNGAQIISPHDKGISQAIEENLE
          GVPVYLFSNITPTPFVPYTVSHLNLCAGIMVTASHNPKQDNGYKVYWDNGAQIISPHDKGISQAIEENLE
Retrocopy GVPVYLFSNITPTPFVPYTVSHLNLCAGIMVTASHNPKQDNGYKVYWDNGAQIISPHDKGISQAIEENLE

Parental  PWTKAWDDSIINNNPLHHDPYSTINNDYFEDLKKYCFHRNIDQSTQLKFVHTSVHGVGHDFVQSAFKAFD
          PWTKAWDDSIINNNPLHHDPYSTINNDYFEDLKKYCFHRNIDQSTQLKFVHTSVHGVGHDFVQSAFKAFD
Retrocopy PWTKAWDDSIINNNPLHHDPYSTINNDYFEDLKKYCFHRNIDQSTQLKFVHTSVHGVGHDFVQSAFKAFD

Parental  FVPPDAVPEQKAPDPEFPTVKYPNPEEGKGVLTLSFALAEKTQAKIILANDPDADRLAVAEQQENGEWKV
          FVPPDAVPEQKAPDPEFPTVKYPNPEEGKGVLTLSFALAEKTQAKIILANDPDADRLAVAEQQENGEWKV
Retrocopy FVPPDAVPEQKAPDPEFPTVKYPNPEEGKGVLTLSFALAEKTQAKIILANDPDADRLAVAEQQENGEWKV

Parental  FSGNEMGALLGWWLFTCWKEKNQDQNALKDLYMLSSTVSSKILRAIALKEGFHFEETLTGFKWMGNRAKQ
          FSGNEMGALLGWWLFTCWKEKNQDQNALKDLYMLSSTVSSKILRAIALKEGFHFEETLTGFKWMGNRAKQ
Retrocopy FSGNEMGALLGWWLFTCWKEKNQDQNALKDLYMLSSTVSSKILRAIALKEGFHFEETLTGFKWMGNRAKQ

Parental  LIDQGKTVLFAFEEAIGYMCCPFVLDKDGVSAAVISAELASFLATKNMSLAQQLKAIYVEYGYHITKASY
          LIDQGKTVLFAFEEAIGYMCCPFVLDKDGVSAAVISAELASFLATKNMSLAQQLKAIYVEYGYHITKASY
Retrocopy LIDQGKTVLFAFEEAIGYMCCPFVLDKDGVSAAVISAELASFLATKNMSLAQQLKAIYVEYGYHITKASY

Parental  FICHDQNIIQNLFENLRNYDGKNNYPKTCGKFEVSGIRDLTTGYDSSQPDKKAILPTSKSSQMITFTFAN
          FICHDQNIIQNLFENLRNYDGKNNYPKTCGKFEVSGIRDLTTGYDSSQPDKKAILPTSKSSQMITFTFAN
Retrocopy FICHDQNIIQNLFENLRNYDGKNNYPKTCGKFEVSGIRDLTTGYDSSQPDKKAILPTSKSSQMITFTFAN

Parental  GGVATLRTSGTEPKIKYYAELCVPPGNSDHEQLKKELDELVSAIEEYFFEPEKNKLQPKSE
          GGVATLRTSGTEPKIKYYAELCVPPGNSDHEQLKKELDELVSAIEEYFFEPEKNKLQPKSE
Retrocopy GGVATLRTSGTEPKIKYYAELCVPPGNSDHEQLKKELDELVSAIEEYFFEPEKNKLQPKSE

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	1.67 RPM	0.00 RPM
SRP007412_cerebellum	2.94 RPM	0.00 RPM
SRP007412_heart	1.20 RPM	0.00 RPM
SRP007412_kidney	5.27 RPM	0.00 RPM
SRP007412_liver	3.02 RPM	0.00 RPM
SRP007412_testis	16.50 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_110 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_110 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.

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011458	1 retrocopy	retro_chof_612,
Microcebus murinus	ENSMICG00000012334	1 retrocopy	retro_mmur_1240,
Monodelphis domestica	ENSMODG00000020527	1 retrocopy	retro_mdom_110 ,