RetrogeneDB ID: retro_mmur_552

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: GeneScaffold_3825:7443..8609(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: SMAD4
• Ensembl ID: ENSMICG00000017525
• Aliases: None
• Description: SMAD family member 4 [Source:HGNC Symbol;Acc:6770]

Sequence

>retro_mmur_552
CATGACTTTGAGGGACAGCCATCGTTATCCACTGAAGGACATTCAATTCAAACCATCCAGCATCCACCAAGTAATCGTGC
ATCGACAGAGACATACAGCACCCCACCTCTGTTAGCCCCATCTGAGTCTAATGCTACCAGCAACGCCAACTTTCCCAACA
TTCCTGTGGCTTCCACAAGTCAGCCTGCTAGTATACTAGCAGGCAGCCATAGTGAAGGACTGTTGCAGATAGCATCAGGG
CCTCAGCCAGGACAGCAGCAGAATGGATTTACTGGTCAGCCAGCTACTTACCATCATAACAGCACTACCACCTGGACTGG
AAGTAGGACTGCACCATACACACCTAATTTGCCTCACCACCAAAACGGCCATCTTCAGCACCACCCGCCTATGCTGCCCC
ATCCCGGACATTACTGGCCAGTTCACAATGAACTTGCATTCCAGCCTCCCATTTCCAATCATCCTGCTCCTGAGTATTGG
TGTTCCATTGCTTACTTTGAAATGGATGTTCAGGTAGGAGAGACATTTAAGGTTTCTTCAAGCTGCCCTATCGTTACTGT
TGATGGGTATGTGGACCCTTCAGGAGGAGATCGCTTTTGCTTGGGTCAACTCTCCAATGTCCACAGGACAGAAGCCATTG
AGAGAGCAAGGTTGCACATAGGCAAAGGTGTGCAGTTGGAATGTAAAGGTGAAGGTGACGTTTGGGTCAGGTGCCTCAGT
GACCACATGGTCTTTGTACAGAGTTACTACTTAGACAGAGAAGCTGGGCGTGCACCTGGAGATGCTGTTCATAAGATCTA
CCCCAGTGCATATATAAAGGTCTTGATTTGCGTCAGTGTCATCGACAGATGCAGCAGCAGGCGGCCACTGCACAAGCTGC
AGCCGCCGCCCAGGCAGCAGCCGTGGCAGGAAACATCCCTGGTCCAGGATCAGTAGGTAGAATAGCTCCAGCTATCAGTC
TATCAGCTGCTGCGGGAATTGGTGTTGATGACCTTCGTCGCTTATGCATACTCAGGATGAGTTTTGTGAAAGGCTAGGGA
CCGGATTACTCAAGACAGAGCATCAAGGAGACCCCTTGCTGGATTGAAATTCACTTACACCGGGCCCTCCAGCTCCTAGA
TGAAGTACTTCACACCATGCCAATTGCAGACCCACAGCCTCTAGAC

Alignment

ORF - retro_mmur_552 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.08 %
• Parental protein coverage: 70.47 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HDFEGQPSLSTEGHSIQTIQHPPSNRASTETYSTPALLAPSESNATSNANFPNIPVASTSQPASILAGSH
          HDFEGQPSLSTEGHSIQTIQHPPSNRASTETYSTP.LLAPSESNATSNANFPNIPVASTSQPASILAGSH
Retrocopy HDFEGQPSLSTEGHSIQTIQHPPSNRASTETYSTPPLLAPSESNATSNANFPNIPVASTSQPASILAGSH

Parental  SEGLLQIASGPQPGQQQNGFTGQPATYHHNSTTTWTGSRTAPYTPNLPHHQNGHLQHHPPMPPHPGHYXX
          SEGLLQIASGPQPGQQQNGFTGQPATYHHNSTTTWTGSRTAPYTPNLPHHQNGHLQHHPPM.PHPGHY..
Retrocopy SEGLLQIASGPQPGQQQNGFTGQPATYHHNSTTTWTGSRTAPYTPNLPHHQNGHLQHHPPMLPHPGHYWP

Parental  XXXXXXXXXXXXXXXXPEYWCSIAYFEMDVQVGETFKVPSSCPIVTVDGYVDPSGGDRFCLGQLSNVHRT
          ................PEYWCSIAYFEMDVQVGETFKV.SSCPIVTVDGYVDPSGGDRFCLGQLSNVHRT
Retrocopy VHNELAFQPPISNHPAPEYWCSIAYFEMDVQVGETFKVSSSCPIVTVDGYVDPSGGDRFCLGQLSNVHRT

Parental  EAIERARLHIGKGVQLECKGEGDVWVRCLSDHAVFVQSYYLDREAGRAPGDAVHKIYPSAYIKV-FDLRQ
          EAIERARLHIGKGVQLECKGEGDVWVRCLSDH.VFVQSYYLDREAGRAPGDAVHKIYPSAYIKV..DLRQ
Retrocopy EAIERARLHIGKGVQLECKGEGDVWVRCLSDHMVFVQSYYLDREAGRAPGDAVHKIYPSAYIKV<LDLRQ

Parental  CHRQMQQQAATAQAAAAAQAAAVAGNIPGPGSVGGIAPAISLSAAAGIGVDDLRRLCILRMSFVKGWGPD
          CHRQMQQQAATAQAAAAAQAAAVAGNIPGPGSVG.IAPAISLSAAAGIGVDDLRRLCILRMSFVKG.GPD
Retrocopy CHRQMQQQAATAQAAAAAQAAAVAGNIPGPGSVGRIAPAISLSAAAGIGVDDLRRLCILRMSFVKG*GPD

Parental  YPRQSIKETPCWIEIHLHRALQLLDEVLHTMPIADPQPLD
          Y.RQSIKETPCWIEIHLHRALQLLDEVLHTMPIADPQPLD
Retrocopy YSRQSIKETPCWIEIHLHRALQLLDEVLHTMPIADPQPLD

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Microcebus murinus was not studied using RNA-Seq expression data.

ChIP-Seq

Microcebus murinus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmur_552 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_552 was not experimentally validated.

Homology

Retrocopy orthology:

Microcebus murinus 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
Microcebus murinus	ENSMICG00000017525	1 retrocopy	retro_mmur_552 ,