RetrogeneDB ID: retro_lafr_635

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_27:14578121..14578876(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TYMS
• Ensembl ID: ENSLAFG00000014910
• Aliases: None
• Description: Thymidylate synthase [Source:UniProtKB/TrEMBL;Acc:G3TE40]

Sequence

>retro_lafr_635
TTGGCATGCAGGCACAACCTAAGAGATGAGCTTTCTTCGCGGACAACCAAGCTTGTGTTCTGCAGGGCTGTTTTGGAGGA
GTTGCTGTGTCTTATCAAGGAATCCACCAATGCTAAAGAACTGTCTTCCAAGGGACTGAAGATCTGGGATGCCAGTGGAT
CCTGAGACTTTTTGGACAGCCTGGGACTCTCCACCTGAGAACAAGGAGATTCAGGCCCAGTTTATGGCTTTCAGTGGAGG
CATTTTGGGGCCGAATATAAAGATCTGAATTCAGATTATATAGGTCAAGGAGTAGACCAGCTGCAAAAGGCTACTGACAC
AATCAAAACCAACCCTGACGACAGAAGAATCTTCATGTGTGTTTGGAATCTAAAAGGCCTTCCTCAGATGGCACTGCCTC
CCTGCCATGCTCTTTGCCAGTTCTGTGAGGTGAACATTGGGCTGTCCTGCTAGCTGTACTAGGGTTCAGGAGACAGGGGC
TTGGAGGTGCCTTTCACCATCGCCAGGTATGCCTGGCTCACCTGTGATTGCACACATCACGGGCCTGAAGCCAGGTGACT
TTGTATATACTTTGGGAGATGCACTCATTTACCTGAATCACACTGAGCTGCTGAAAGTTTAGCTCCAGCGAGAACCAGGA
CCTTTCCCCAAGCTCAAAATTCTTCAGAAGGTTGAAACAACTGGTGATTTCAAAGCTGAAGACTTTTCAGATTGAAGGGT
ACAATCCTCATCTGACTGTTCAAATGGAAATGGCT

Alignment

ORF - retro_lafr_635 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.76 %
• Parental protein coverage: 82.62 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MQARYSLRDEFPLLTTKRVFWKGVLEELLWFIKGSTNAKELSSKGVKIWDANGSRDFLDSLGFSAREEGD
          ...R..LRDE....TTK.VF...VLEELL..IK.STNAKELSSKG.KIWDA.GS.DFLDSLG.S..E.GD
Retrocopy LACRHNLRDELSSRTTKLVFCRAVLEELLCLIKESTNAKELSSKGLKIWDASGS*DFLDSLGLST*EQGD

Parental  LGPVYGFQWRHFGAKYKDMNSDYSGQGVDQLQKVIDTIKTNPDDRRIIMCAWNPKDLAQMALPPCHALCQ
          .GPVYGFQWRHFGA.YKD.NSDY.GQGVDQLQK..DTIKTNPDDRRI.MC.WN.K.L.QMALPPCHALCQ
Retrocopy SGPVYGFQWRHFGAEYKDLNSDYIGQGVDQLQKATDTIKTNPDDRRIFMCVWNLKGLPQMALPPCHALCQ

Parental  FYVVNGELSCQLYQRSGD-MGLGVPFNIASYSLL-TYMIAHITGLKPGDFVHTLGDAHIYLNHIEPLKVQ
          F..VN..LSC.LY..SGD..GLG..F......L.....IAHITGLKPGDFV.TLGDA.IYLNH.E.LKV.
Retrocopy FCEVNIGLSC*LY*GSGD<QGLGGAFHHRQVCLA<SPVIAHITGLKPGDFVYTLGDALIYLNHTELLKV*

Parental  LQREPRPFPKLNILRKVDTIDAFKAED-FQIEGYNPHPTIKMEMA
          LQREP.PFPKL.IL.KV.T...FKAED.FQIEGYNPH.T..MEMA
Retrocopy LQREPGPFPKLKILQKVETTGDFKAED>FQIEGYNPHLTVQMEMA

Legend:

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

Expression

RNA-Seq

Loxodonta africana was not studied using RNA-Seq expression data.

ChIP-Seq

Loxodonta africana was not studied using ChIP-Seq data.

EST

Loxodonta africana was not studied using EST data.

TSS

Loxodonta africana was not studied using FANTOM5 data.

Lab

retro_lafr_635 was not experimentally validated.

Homology

Retrocopy orthology:

Loxodonta africana 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,