RetrogeneDB ID: retro_mluc_2502

Retrocopy location

• Organism: Microbat (Myotis lucifugus)
• Coordinates: GL430580:195295..196429(+)
• Located in intron of: ENSMLUG00000023576

Retrocopy information

• Ensembl ID: ENSMLUG00000010989
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PHGDH
• Ensembl ID: ENSMLUG00000002986
• Aliases: None
• Description: None

Sequence

>retro_mluc_2502
AGGATCAGGAGAGAGGTGGCCGTCCGGAGGCAGTCCTTGGGGATGAAAACTGTAGGGTATGACCCCATCATCTCACCAGA
GGTCTCGGCCTCCTTCGGCGTTCAGCAGCTGCCCCTGGAGGAGATCTGGCCCCTCTGTGACTTCATCATTGTGCACACCC
CTCTCCTGCCCTCCACGACAGGCCTGCTGAACCACTTCACCTTCGCCCTGTGCAAGAAGGGCGTGCGCGTGGTGAACTGC
GCCCGCGGAGGGATCGTGAACGAGATTGCCCTGCTCCGGGCCCTGCAGTCAGGGCAGTGCGCGAGTGCAGCGCTGGACAT
GTTCACTGAGGAGCCACCGCTGGACCGTGCCTTGGTGGACCATGAGAATGTCATCAGCTGCCCCCACCTGGGCGCCAGCA
CCAAGGAGGCCCAGAGCCGCTGCCGGAGGAGATCGCTGTCCAGTTCGTGGACATGGTGAAGGGGAGAGCCCTTGCGGGGG
TTGTGAATGCCCAGGCCCTTACCATCGCCTTCTCTCAGCACACCAAACCTTGGCTCGGTCTGGCCGAAGCTCTGGGGACT
CTGATGCGAGCCTGGGCAGGGTCCCCCAAAGGGACCATCCAGGTGGTAACGCAGGGCTTATCCCTGAAGAATGCTGGGAA
CTGCCTGAGCCCCGCAGTCATTGTCGGCCTCCTCAAAGACGCTTCCAATCATGCGGATATGAACTTGGTGAACACCAAGC
TGCTGGTGAAGGAGGGCGGCCTCAGTGTAACCTTCTCCCATAACCCCGCTGTGCCAGGAGAGCAAGGACGCAGGGAAGGC
CTCCTGAGCGTGGCCCTGGCAGGTGCCCCCTACGAGGCTGTGGGCTTTGTCCAGGGCACCACACCTGTGCTGCAGGCACT
CAACGGAGCTGCCTCAGACCAGAAGTGCCTCTCAGCAGGGGTCTGCCCCTGCTCCTGTTCCGGGCTCAGCCCTCCAACCC
TGCCTGCTGCCTACCATGATTGGGCTCCTGGCAGAGGCAGATGTGCAGCTGCTGTCCTACCAGACCTCGCTGGTGTCCGA
CGGGGAGACCTGGCACCTCATGGGCATCTCTTCCCTGCTGCCCAGCCTGGACACCTGGAAGCAGCATGTGACCGAGGCCT
TTCAGTTCCATTTC

Alignment

ORF - retro_mluc_2502 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.32 %
• Parental protein coverage: 71.21 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RIGREVAVRMQSFGMKTVGYDPIISPEVSASFGVQQLPLEEIWPLCDFITVHTPLLPSTTGLLNDSTFAL
          RI.REVAVR.QS.GMKTVGYDPIISPEVSASFGVQQLPLEEIWPLCDFI.VHTPLLPSTTGLLN..TFAL
Retrocopy RIRREVAVRRQSLGMKTVGYDPIISPEVSASFGVQQLPLEEIWPLCDFIIVHTPLLPSTTGLLNHFTFAL

Parental  CKKGVRVVNCARGGIVDEGALLRALQSGQCAGAALDVFTEEPPRDRALVDHENVISCPHLGASTKEAQSR
          CKKGVRVVNCARGGIV.E.ALLRALQSGQCA.AALD.FTEEPP.DRALVDHENVISCPHLGASTKEAQSR
Retrocopy CKKGVRVVNCARGGIVNEIALLRALQSGQCASAALDMFTEEPPLDRALVDHENVISCPHLGASTKEAQSR

Parental  C-GEEIAVQFVDMVKGRALAGVVNAQALTSAFSPHTKPWLGLAEALGTLMRAWAGSPKGTIQVVTQGERG
          C..EEIAVQFVDMVKGRALAGVVNAQALT.AFS.HTKPWLGLAEALGTLMRAWAGSPKGTIQVVTQG...
Retrocopy C<PEEIAVQFVDMVKGRALAGVVNAQALTIAFSQHTKPWLGLAEALGTLMRAWAGSPKGTIQVVTQGL--

Parental  TLQREXDCLSPAVIVGLLRDASNHADVNLVNAKLLVKEAGLNVTSSHNPAVPGEQGCGEGLLSVALAGAP
          .L.....CLSPAVIVGLL.DASNHAD.NLVN.KLLVKE.GL.VT.SHNPAVPGEQG..EGLLSVALAGAP
Retrocopy SLKNAGNCLSPAVIVGLLKDASNHADMNLVNTKLLVKEGGLSVTFSHNPAVPGEQGRREGLLSVALAGAP

Parental  YEAVGFVQGTTPVLQALNGAA-FRPEVPLRRGLPLLLFRAQPSNPA-MLPTMIGLLAEAGVQLLSYQTSV
          YEAVGFVQGTTPVLQALNGAA..RPEVPL.RGLPLLLFRAQPSNPA..LPTMIGLLAEA.VQLLSYQTS.
Retrocopy YEAVGFVQGTTPVLQALNGAA<LRPEVPLSRGLPLLLFRAQPSNPA<LLPTMIGLLAEADVQLLSYQTSL

Parental  VSDGETWHVMGISSLLPSLDAWKQHVTEAFQFHF
          VSDGETWH.MGISSLLPSLD.WKQHVTEAFQFHF
Retrocopy VSDGETWHLMGISSLLPSLDTWKQHVTEAFQFHF

Legend:

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

Expression

RNA-Seq

Myotis lucifugus was not studied using RNA-Seq expression data.

ChIP-Seq

Myotis lucifugus was not studied using ChIP-Seq data.

EST

Myotis lucifugus was not studied using EST data.

TSS

Myotis lucifugus was not studied using FANTOM5 data.

Lab

retro_mluc_2502 was not experimentally validated.

Homology

Retrocopy orthology:

Myotis lucifugus 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 4 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019916	4 retrocopies	retro_cjac_2894, retro_cjac_2958, retro_cjac_3441, retro_cjac_3994,
Myotis lucifugus	ENSMLUG00000002986	1 retrocopy	retro_mluc_2502 ,
Mus musculus	ENSMUSG00000053398	16 retrocopies	retro_mmus_1008, retro_mmus_1223, retro_mmus_1384, retro_mmus_1708, retro_mmus_1835, retro_mmus_1892, retro_mmus_2057, retro_mmus_2169, retro_mmus_2889, retro_mmus_2979, retro_mmus_3021, retro_mmus_3176, retro_mmus_3180, retro_mmus_3217, retro_mmus_3441, retro_mmus_545,
Rattus norvegicus	ENSRNOG00000019328	1 retrocopy	retro_rnor_452,