RetrogeneDB ID: retro_lafr_326

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_12:43540551..43541901(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUBA1B
• Ensembl ID: ENSLAFG00000010021
• Aliases: None
• Description: None

Sequence

>retro_lafr_326
CGTGAGTGCATCTCCATCCACGTAGGCCAGGCTGGTGTCCAGATTGGCAACACCTGCTGGGAGCTCTACTGTCTGGAACA
CGGCATTCAGCCTGATGGCTAGATGCCAAGTGACAAGACCATTGGGGGAGGAGACGACTCCTTCAACACCTTCTTCAGTG
AGACAGGCACTGGCAAGCATGTTCCCAGGGCAATGTTTGTAGACCTGGAACCCACGGTCATTGATGAAGTTTGCACTGGC
ACCTACCGCCAGCTCTTCCATCCTGAGCAGCTCATCACAGGCAAGGAAGATGCTGCCAATAACTATGCCCACGGCCACTA
CACCATCAGCAAGGAGATCACTGACCTTGTCTTGGACAGAATTCACAAGCTGGCTGACCAGTGCACAGGTCTTCAGGGCT
TCTTGGTTTTCCACAGCTTTGGTGGGGGAACCGGTTCTGGGTTCACCTATTTGCTGATGGAACGTCTCTCAGTTGATTAT
GGCAAGAAGTCCAAGCTGGAGTTCTCTATTTACCCAGCCCCCCAGGTTTCCACAGCTGTAGTTGGGCCCTACCACTCCAT
CCTCACCACCCACACCACCCTGGAGCACTCAGATTGTGCCTTCGTGGTAGACAATGAGGCCATCTATGACATCTGTCGCA
GAAACCTTGATATTGAGCACCCAACCTATACTAACCTTAACCGCCTTATTAGCCAGATTGTGTCCTCTATCACTGCTTCC
TTCAGATTTGATGGTGCCCTGAATGTCAATCTGACAGAATTCCAGACCAACCTGGTGCCCTATCCCTGCATCCACTTCCC
TCTGGCCACATATGCCCCTGTCATCTCTGCTGAGAAAGCCTACCATGAACAGCTTTCTGTAGCAGAGATTACCAATGCTT
GCTTTGAGCCAGCCAACCAGATGGTGAAATGTGACCCCCGCCATGGTAAATACATGGCTTGCTGCCTGTTGTACCACGGT
AATGTGGTTCCCAAAGATGTCAATGCTGCCATTGCCACCATCAAGACCAAGCACAGCATCCAGTTTGTGGATTGGTGCCC
CACTGGCTTCAAGGTTCGCATTAACTACCAGCCTCCCACTGTGGTGCCTGGTGGAGACCTGGCCAAGGTACAGCGAGCTG
TGTGCATGCTGAGCAACACCACAGCCATTGTTGAGGCCTGGGCTCGCCTGGACCACAAGTTTGACCTGATGTATGCCAAG
CATGCCTTTGTTCACTGGTACGTGGGTGATGGGATGGAGGAAGGAGAGTTTTCTGAGGCCTGTGAGGACATGGCTGCCCT
TGAGAAGGACTATGAGGAGGTTGGTGTGGATTCTGTTGAAGGAGAGAGTGAGGAAGAAGGAGAAGAATAC

Alignment

ORF - retro_lafr_326 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.22 %
• Parental protein coverage: 99.78 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLE
          RECISIHVGQAGVQIGN.CWELYCLEHGIQPDG.MPSDKTIGGGDDSFNTFFSETG.GKHVPRA.FVDLE
Retrocopy RECISIHVGQAGVQIGNTCWELYCLEHGIQPDG*MPSDKTIGGGDDSFNTFFSETGTGKHVPRAMFVDLE

Parental  PTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSF
          PTVIDEV.TGTYRQLFHPEQLITGKEDAANNYA.GHYTI.KEI.DLVLDRI.KLADQCTGLQGFLVFHSF
Retrocopy PTVIDEVCTGTYRQLFHPEQLITGKEDAANNYAHGHYTISKEITDLVLDRIHKLADQCTGLQGFLVFHSF

Parental  GGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYD
          GGGTGSGFT.LLMERLSVDYGKKSKLEFSIYPAPQVSTAVV.PY.SILTTHTTLEHSDCAF.VDNEAIYD
Retrocopy GGGTGSGFTYLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVGPYHSILTTHTTLEHSDCAFVVDNEAIYD

Parental  ICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKA
          ICRRNLDIE.PTYTNLNRLISQIVSSITAS.RFDGALNV.LTEFQTNLVPYP.IHFPLATYAPVISAEKA
Retrocopy ICRRNLDIEHPTYTNLNRLISQIVSSITASFRFDGALNVNLTEFQTNLVPYPCIHFPLATYAPVISAEKA

Parental  YHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGF
          YHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLY.G.VVPKDVNAAIATIKTK.SIQFVDWCPTGF
Retrocopy YHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYHGNVVPKDVNAAIATIKTKHSIQFVDWCPTGF

Parental  KVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEA
          KV.INYQPPTVVPGGDLAKVQRAVCMLSNTTAI.EAWARLDHKFDLMYAK.AFVHWYVG.GMEEGEFSEA
Retrocopy KVRINYQPPTVVPGGDLAKVQRAVCMLSNTTAIVEAWARLDHKFDLMYAKHAFVHWYVGDGMEEGEFSEA

Parental  REDMAALEKDYEEVGVDSVEGEGEEEGEEY
          .EDMAALEKDYEEVGVDSVEGE.EEEGEEY
Retrocopy CEDMAALEKDYEEVGVDSVEGESEEEGEEY

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_326 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 13 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006872	4 retrocopies	retro_amel_1162, retro_amel_1367, retro_amel_1387, retro_amel_1895,
Canis familiaris	ENSCAFG00000008640	8 retrocopies	retro_cfam_1481, retro_cfam_1751, retro_cfam_1895, retro_cfam_1917, retro_cfam_1979, retro_cfam_2000, retro_cfam_463, retro_cfam_926,
Choloepus hoffmanni	ENSCHOG00000008444	2 retrocopies	retro_chof_179, retro_chof_360,
Cavia porcellus	ENSCPOG00000013016	1 retrocopy	retro_cpor_96,
Felis catus	ENSFCAG00000027011	1 retrocopy	retro_fcat_588,
Felis catus	ENSFCAG00000028689	3 retrocopies	retro_fcat_1802, retro_fcat_254, retro_fcat_798,
Loxodonta africana	ENSLAFG00000010021	1 retrocopy	retro_lafr_326 ,
Microcebus murinus	ENSMICG00000017551	3 retrocopies	retro_mmur_144, retro_mmur_705, retro_mmur_885,
Myotis lucifugus	ENSMLUG00000002622	4 retrocopies	retro_mluc_154, retro_mluc_186, retro_mluc_234, retro_mluc_270,
Otolemur garnettii	ENSOGAG00000009435	1 retrocopy	retro_ogar_240,
Tupaia belangeri	ENSTBEG00000001671	1 retrocopy	retro_tbel_3700,
Tarsius syrichta	ENSTSYG00000013266	7 retrocopies	retro_tsyr_1014, retro_tsyr_1278, retro_tsyr_1281, retro_tsyr_1679, retro_tsyr_1834, retro_tsyr_243, retro_tsyr_6,
Tursiops truncatus	ENSTTRG00000004794	1 retrocopy	retro_ttru_407,