RetrogeneDB ID: retro_mdom_514

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:121263345..121264517(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000019446
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CDH13
• Ensembl ID: ENSMODG00000015029
• Aliases: None
• Description: cadherin 13, H-cadherin (heart) [Source:HGNC Symbol;Acc:1753]

Sequence

>retro_mdom_514
ACTCTGGAAAACCCTAAATATGAACTGATCATTGAAGCTCAGGACATGGCTGGTTTGGACGTTGGTTTAACTGGGACAGC
AACAGCTACCATTCTGATTGATGACAAAAATGATCACTCCCCAAAGTTCACCAAGAAAGAGTTTCATGCCATTGTCAATG
AAGGAGTTGTGGGAGTGATTGTCAATTTAACAGTCCAAGATAAGGATGACCCTACTACTGCAGTCTGGAGAGCAGTCTAC
ACTATCATCAATGGAAATCCAGGGCAAAGTTTTGAAATACATACGAATCCCCAAACCAACGAGGGAATGCTTTCTGTTGT
CAAACCTTTGGATTATGAGATTTCAGCATTTCACACACTATTGATCAAAGTAGAAAATGAAGACCCATTGGTTCTTGATG
TAGCATATGCCCCAGCTCTACAGCCACAGTCCAGATAACTGTCTCGGATGTAAATGAAGGCCCAGTTTTTCACCCTGACC
CCATGACAGTGACCAAGCGTGAGAACATCACTATTGGCAGCATGCTGTTGACAGTAAATGCCACAGATCCTGATTCCTTG
CAGCATCAGACCATTAGGTACTCTATTTATAAAGATCCAGTAGGATGGCTATACATCAACCCAATCAATGGGACAATTGA
TACAGCAGCTGTCTTGGACCGTGAATCTCCATTTGTCCACAATAATATATACACTGCACTTTTCCTTGCAATAGATAGTG
GTGATCCTCCTGCAACTGGCACTGGAACTCTACAGATAAAACTGGAAGATGTGAATGACAATGCTCCTCTTATTTACCCC
ACACTTGCCAAAGTTTGTGATGATGCCAGAGATCTCAATGTGGTCATTCTGGGTGCATCAGATAAGGATCTCCACCCAAA
TACTGATCCATTCAAATTTGAATTGAATAAACAAACTGGGTCTGATAAATTCTGGAAAATTTCTAAGATCAATGACACTC
ATGCCCAGGTAAGCCTTCTTCAGAACCTGAAGAAAGCCAACTACAAACTACCTGTCATGGTGACAGACTCGGGCACGCCA
CCTTTGTCAAACACCACAGAACTAAGAGTGCAAGTTTGTTCCTGTAAGAAATCTAAAATGGACTGCAGCTCAGCTGGGAT
CCCGCATATCAGAACCACCTTAGTTCTGCTTCTTTCATTCTTCAGCTTAGTA

Alignment

ORF - retro_mdom_514 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.7 %
• Parental protein coverage: 59.42 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TLENPKYELIIEAQDMAGLDVGLTGTATATILIDDKNDHSPKFTKKEFHATVNEGVVGVIVNLTVEDKDD
          TLENPKYELIIEAQDMAGLDVGLTGTATATILIDDKNDHSPKFTKKEFHA.VNEGVVGVIVNLTV.DKDD
Retrocopy TLENPKYELIIEAQDMAGLDVGLTGTATATILIDDKNDHSPKFTKKEFHAIVNEGVVGVIVNLTVQDKDD

Parental  PTTAAWRAVYTIINGNPGQSFEIHTNPQTNEGMLSVVKPLDYEISAFHTLLIKVENEDPLVPDVAYGP-S
          PTTA.WRAVYTIINGNPGQSFEIHTNPQTNEGMLSVVKPLDYEISAFHTLLIKVENEDPLV.DVAY.P.S
Retrocopy PTTAVWRAVYTIINGNPGQSFEIHTNPQTNEGMLSVVKPLDYEISAFHTLLIKVENEDPLVLDVAYAP<S

Parental  STATVQITVSDVNEGPVFHPDPMTVTKRENITIGSMLLTVNATDPDSLQHQTIRYSIYKDPAGWLYINPI
          STATVQITVSDVNEGPVFHPDPMTVTKRENITIGSMLLTVNATDPDSLQHQTIRYSIYKDP.GWLYINPI
Retrocopy STATVQITVSDVNEGPVFHPDPMTVTKRENITIGSMLLTVNATDPDSLQHQTIRYSIYKDPVGWLYINPI

Parental  NGTIDTAAVLDRESPFVHNNIYTALFLAIDSGDPPATGTGTLQIKLEDVNDNAPLIYPTLAKVCDDAKDL
          NGTIDTAAVLDRESPFVHNNIYTALFLAIDSGDPPATGTGTLQIKLEDVNDNAPLIYPTLAKVCDDA.DL
Retrocopy NGTIDTAAVLDRESPFVHNNIYTALFLAIDSGDPPATGTGTLQIKLEDVNDNAPLIYPTLAKVCDDARDL

Parental  NVVILGASDKDLHPNTDPFKFELNKQTGSDKFWKISKINDTHAQVSLLQNLKKANYNLPVMVTDSGTPPL
          NVVILGASDKDLHPNTDPFKFELNKQTGSDKFWKISKINDTHAQVSLLQNLKKANY.LPVMVTDSGTPPL
Retrocopy NVVILGASDKDLHPNTDPFKFELNKQTGSDKFWKISKINDTHAQVSLLQNLKKANYKLPVMVTDSGTPPL

Parental  SNTTELRVQVCSCKKSKMDCSSAGIPHIRTTLVLLLSFFSLV
          SNTTELRVQVCSCKKSKMDCSSAGIPHIRTTLVLLLSFFSLV
Retrocopy SNTTELRVQVCSCKKSKMDCSSAGIPHIRTTLVLLLSFFSLV

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	0.12 RPM	86.78 RPM
SRP007412_cerebellum	0.00 RPM	63.33 RPM
SRP007412_heart	0.40 RPM	408.27 RPM
SRP007412_kidney	0.00 RPM	14.49 RPM
SRP007412_liver	0.00 RPM	1.01 RPM
SRP007412_testis	0.00 RPM	24.55 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_514 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_514 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000015029	1 retrocopy	retro_mdom_514 ,