RetrogeneDB ID: retro_mmur_276

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: GeneScaffold_2141:135384..136826(+)
• Located in intron of: ENSMICG00000017894

Retrocopy information

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

Parental gene information

• Parental gene symbol: RYK
• Ensembl ID: ENSMICG00000004507
• Aliases: None
• Description: receptor-like tyrosine kinase [Source:HGNC Symbol;Acc:10481]

Sequence

>retro_mmur_276
AGCGTGAGCCTCTACCTGAGCGAGGACGAGGTGAGCCGGCTGATCGGTCTTGATGCAGAACTTTATTATGTGAGAAACGA
CCTCATTAGTCACTGTGCTCTATCTTTTAACCTGTTAGTACCCAGTGAGACAAATTTCCTGCACTTCACTTGGCATGCAA
AGTCCAAGGTTGAATATAAGCTAGGATTCCAAGTAGACCATTTTGTGGCTATGGACATGCCGCAGGTCAACATTTCTGTT
CAGGGGGAGGTTCCACGCACTTTATCAGTGTTTCCGGTCGAGCTTTCCTGTACTGGCAAAGTAGATTCTGAAGTTATGAT
ACTTATGCAGCTCAATTTGACAGTAAATTCTTCAAAAAATTTTACAGTCCTAAATTTTAAGCGAAGGAAAATGTGCTACA
AAAAACTTGAAGAAGTAAAAACTTCAGCTTTGGACAAAAACACTAGCAGAACTATTTATGATCCTGTACATGCAGCTCCA
ACCACTTCTACGCGTGTGTTTTATATCAGTGTAGGGGTTTGTTGTGCAGTTATATTTCTTGTAGCAGTAATATTAGCTGT
TTTGCACCTTCATAGTATGAAAAGGATTGAACTGGATGACAGCATCAGTGCCAGCAGTAGTTCCCAAGGGCTGTCTCAGC
CTTCCACCCAGACAACTCAGTATCTGAGAGCTGACACACCCAACAATGCAACTCCTACCTCCAGCTCCTCAGGTTACCCT
ACCTTGCGGATAGAGAAGAACGACCTGAGAAGTGTCACTCTTTTGGAGGCCAAAGCCAAGGTGAAGGATATAGCAATATC
CAGGGAGAGGATAACTCTGAAAGATGTGCTCCAAGAAGGTACTTTGGGGCGTATTTTCCATGGGATTTTAGTAGATGAAA
AAGATCCAAATAAAGAAAAACAAGCATTTGTAAAAACAGTTAAAGATCAAGCTTCTGAAATTCAGGTGACGATGATGCTC
ACTGAAAGTTGTAAGCTGCGAGGTCTTCATCACAGAAATCTTCTTCCTATTACTCATGTGTGTATAGAAGAAGGAGAAAA
GCCCATGGTGATATTGCCTTACATGAATTGGGGGAATCTTAAATTGTTTTACGGCAGTACAAATTAGTAGAGGCCAATAA
TCCACAGGCAATTTCTCAGCAAGACCTGGTACACATGGCTATTCAGATTGCCTGTGGAATGAGCTACCTGGCCAGAAGGG
AAGTCATCCACAAAGACCTGGCTGCTAGGAACTGTGTCATTGATGACACACTTCAAGTTAAGATCACAGATAATGCTCTC
TCCAGAGACTTATTTCCCATGGACTATCACTGTTTGGGGGATAATGAAAATAGGCCCGTTCGGTGGATGGCTCTTGAAAG
TCTGGTTAATAATGAGTTCTCCAGCGCTAGTGATGTGTGGGCCTTTGGAGTGACGCTGTGGGAGCTTATGACTCTGGGCC
AG

Alignment

ORF - retro_mmur_276 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.95 %
• Parental protein coverage: 80.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SVSLYLSEDEVRRLIGLDAELYYVRNDLISHYALSFNLLVPSETNFLHFTWHAKSKVEYKLGFQVDNFVA
          SVSLYLSEDEV.RLIGLDAELYYVRNDLISH.ALSFNLLVPSETNFLHFTWHAKSKVEYKLGFQVD.FVA
Retrocopy SVSLYLSEDEVSRLIGLDAELYYVRNDLISHCALSFNLLVPSETNFLHFTWHAKSKVEYKLGFQVDHFVA

Parental  MDMPQVNISVQGEVPRTLSVFRVELSCTGKVDSEVMILMQLNLTVNSSKNFTVLNFKRRKMCYKKLEEVK
          MDMPQVNISVQGEVPRTLSVF.VELSCTGKVDSEVMILMQLNLTVNSSKNFTVLNFKRRKMCYKKLEEVK
Retrocopy MDMPQVNISVQGEVPRTLSVFPVELSCTGKVDSEVMILMQLNLTVNSSKNFTVLNFKRRKMCYKKLEEVK

Parental  TSALDKNTSRTIYDPVHAAPTTSTRVFYISVGVCCAVIFLVAIILAVLHLHSMKRIELDDSISA-SSSQG
          TSALDKNTSRTIYDPVHAAPTTSTRVFYISVG.............AVLHLHSMKRIELDDSISA.SSSQG
Retrocopy TSALDKNTSRTIYDPVHAAPTTSTRVFYISVGXXXXXXXXXXXXXAVLHLHSMKRIELDDSISASSSSQG

Parental  LSQPH-QTTQYLRADTPNNATPITSKS-YP-LRIEKNDLRSVT-LEAKAKVKDIAISRERITLKDVLQEG
          LSQP..QTTQYLRADTPNNATP..S.S.YP.LRIEKNDLRSVT.LEAKAKVKDIAISRERITLKDVLQEG
Retrocopy LSQPSTQTTQYLRADTPNNATPTSSSSGYPTLRIEKNDLRSVTLLEAKAKVKDIAISRERITLKDVLQEG

Parental  TFGRIFHGILVDEKDPNKEKQAFVKTVKDQASEIQVTMMLTESCKLRGLHHRNLLPITHVCIEEGEKPMV
          T.GRIFHGILVDEKDPNKEKQAFVKTVKDQASEIQVTMMLTESCKLRGLHHRNLLPITHVCIEEGEKPMV
Retrocopy TLGRIFHGILVDEKDPNKEKQAFVKTVKDQASEIQVTMMLTESCKLRGLHHRNLLPITHVCIEEGEKPMV

Parental  ILPYMNWGNLKLF-LRQCKLVEANNPQAISQQDLVHMAIQIACGMSYLARREVIHKDLAARNCVIDDTLQ
          ILPYMNWGNLKLF.LRQ.KLVEANNPQAISQQDLVHMAIQIACGMSYLARREVIHKDLAARNCVIDDTLQ
Retrocopy ILPYMNWGNLKLF<LRQYKLVEANNPQAISQQDLVHMAIQIACGMSYLARREVIHKDLAARNCVIDDTLQ

Parental  VKITDNALSRDLFPMDYHCLGDNENRPVRWMALESLVNNEFSSASDVWNFGDALWERMTLDQ
          VKITDNALSRDLFPMDYHCLGDNENRPVRWMALESLVNNEFSSASDVW.FG..LWE.MTL.Q
Retrocopy VKITDNALSRDLFPMDYHCLGDNENRPVRWMALESLVNNEFSSASDVWAFGVTLWELMTLGQ

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_276 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_276 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016999	2 retrocopies	retro_btau_790, retro_btau_793,
Microcebus murinus	ENSMICG00000004507	1 retrocopy	retro_mmur_276 ,