RetrogeneDB ID: retro_ogar_3211

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873742.1:1612243..1613162(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TYMS
• Ensembl ID: ENSOGAG00000024349
• Aliases: None
• Description: thymidylate synthetase [Source:HGNC Symbol;Acc:12441]

Sequence

>retro_ogar_3211
GAGCTCCCGCGCCCGCCGTCACCGTCCCCAGCGCAGGAGCAGGGCGCCGAGCCGCAGCCGGCCCATGGGGAGCTGCAGTA
CCTGGGGCAGATCGAGCACATTCTCCGCTGCAGCTTCAGAAAGGACGACCGCACGGACACCGGCACTCTGTCGGTGTTTG
GCATGCAGGCCCGCTACAGCCGGAAAGATGAATTTCCACTGCTGACAACCAAATGTGTGTTCTGGAAGGGTGTTTTGGAG
GAGTTGCTGTGGTTTATCAAGGGATCCACAAAAGCTAAAGAGCTATCTTCCAAAGGAGTGAAAATCTGGGATGCCAATGG
ACACCGAGACTTTTTGGATAGCCTGGGATTATCCAAAAGAGAAGAAGGTGACTTTGGCCTAGTTTATGGCTTCCAGTGGA
GGCATTTTGGAGCAGAATACAAAGATATGGATTCAGATTATTCAGGTCAAGGAGTTACCAATTGCAGAAAGTGATTGATA
CCATCAAAACCAACCCTGATGACAGAAGAATCATCATGCGTGCTTGGAACCCAAAAGATCTTCCTCTGATGACACTACCT
CCGTGCCATGCCTTCTGCCAGTTCTACGTGGTGAACGGTGAACTGACCGCCAGCTGTACCAGCAGTCAGGAGACACGGGC
CTGGGTGTGCCGTTCAACATTGCCAGCTACTCCCTGCTCACGTACAAGATCACGCACATCACTGGTCTGAAGCCAGGTGA
CTTTGTACATACTTTGGGAGATGCACATATTTACCTGAATCACGTGGAGCCGCTGAAGATTCAGCTTCAGAGAGAACCAA
GACCTTTTCCGAAGCTCAAAATCCTTTGAAAAGTTGAGACAATTGATGATTTCAAAGCTGAAGACTTTAAGATTGAAGGT
TACAATCAGCATCCAACCATTAAAATGGAAATGGCTATT

Alignment

ORF - retro_ogar_3211 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.61 %
• Parental protein coverage: 98.08 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ELPRPPSPPPAQERGAESQPPHGELQYLGQIEHILRCGFRKDDRTGTGTLSVFGMQARYSLRDEFPLLTT
          ELPRPPSP.PAQE.GAE.QP.HGELQYLGQIEHILRC.FRKDDRT.TGTLSVFGMQARYS..DEFPLLTT
Retrocopy ELPRPPSPSPAQEQGAEPQPAHGELQYLGQIEHILRCSFRKDDRTDTGTLSVFGMQARYSRKDEFPLLTT

Parental  KRVFWKGVLEELLWFIKGSTNAKELSSKGVKIWDANGSRDFLDSLGFSKREEGDLGPVYGFQWRHFGAEY
          K.VFWKGVLEELLWFIKGST.AKELSSKGVKIWDANG.RDFLDSLG.SKREEGD.G.VYGFQWRHFGAEY
Retrocopy KCVFWKGVLEELLWFIKGSTKAKELSSKGVKIWDANGHRDFLDSLGLSKREEGDFGLVYGFQWRHFGAEY

Parental  KDMDSDYSGQGVD-QLQKVIDTIKTNPDDRRIIMCAWNPKDLPLMALPPCHALCQFYVVNGELSC-QLYQ
          KDMDSDYSGQGV..QLQKVIDTIKTNPDDRRIIM.AWNPKDLPLM.LPPCHA.CQFYVVNGEL...QLYQ
Retrocopy KDMDSDYSGQGVT<QLQKVIDTIKTNPDDRRIIMRAWNPKDLPLMTLPPCHAFCQFYVVNGELTA<QLYQ

Parental  RSGDMGLGVPFNIASYSLLTYMIAHITGLKPGDFVHTLGDAHIYLNHVEPLKIQLQREPRPFPKLKILRK
          .SGD.GLGVPFNIASYSLLTY.I.HITGLKPGDFVHTLGDAHIYLNHVEPLKIQLQREPRPFPKLKIL.K
Retrocopy QSGDTGLGVPFNIASYSLLTYKITHITGLKPGDFVHTLGDAHIYLNHVEPLKIQLQREPRPFPKLKIL*K

Parental  VETIDDFKAEDFKIEGYNPHPTIKMEMAV
          VETIDDFKAEDFKIEGYN.HPTIKMEMA.
Retrocopy VETIDDFKAEDFKIEGYNQHPTIKMEMAI

Legend:

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

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_3211 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii 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 9 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000009230	2 retrocopies	retro_fcat_1107, retro_fcat_339,
Loxodonta africana	ENSLAFG00000014910	2 retrocopies	retro_lafr_1030, retro_lafr_635,
Macropus eugenii	ENSMEUG00000009507	1 retrocopy	retro_meug_175,
Monodelphis domestica	ENSMODG00000021479	2 retrocopies	retro_mdom_1084, retro_mdom_1186,
Mustela putorius furo	ENSMPUG00000005419	2 retrocopies	retro_mputfur_1155, retro_mputfur_860,
Mus musculus	ENSMUSG00000025747	1 retrocopy	retro_mmus_584,
Otolemur garnettii	ENSOGAG00000024349	2 retrocopies	retro_ogar_2956, retro_ogar_3211 ,
Sarcophilus harrisii	ENSSHAG00000003102	1 retrocopy	retro_shar_424,
Sus scrofa	ENSSSCG00000023869	2 retrocopies	retro_sscr_810, retro_sscr_841,