RetrogeneDB ID: retro_lafr_1162

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_8:57872822..57873761(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ALDH1A1
• Ensembl ID: ENSLAFG00000031532
• Aliases: None
• Description: None

Sequence

>retro_lafr_1162
TCAATGAATGGTGGAAAATTATTTGGCAATTTAGATTTGATGGGCTTTGGAGGGTGCATAAAAACCTCACGCTACCACGT
GGGCTGAGCTGAAAAGATTCAGGGCCAAACAATACCGATTGATGAAAACTTTTTTACTTATACAAGACATAAGCCTATTG
GTATATGTGGCCAAATCATTCCTTGGAATTTCCTGTTGGTTATGCTCATGTGGAAGATAGGGCCTGCCCTTTGTGGAAAT
ACTATGATTGTCAAACCAGCGACGCAAACTCCTCTCACGGCTCTTCATGTTGCATCTTTAATAAAAGAGGCAGGGTTTCC
TCCAAGAGTAGTGAATATTGTGCCTGGTTATAGGCCACCACAGGAGCAGCCATTTCTTCCCACATGGACATCAAAAAAGT
GACATTCACAGGATCAATGGAGGTTGGCAAAATGCTCAAAGAAGCTGTTGAGAAAAGCAATCTGAAGAGGGTGACCCTTG
AGCTGGGTGGAAAGACCCCCTGCATTGTGTTTGCTGATGGTGACTTGGACTATGCAGTTGCATTTGCACGCCAGGGATTA
TTTTACCACCAGGGTCAGTGTTGTATAGCTGTATCCAGGCTTTTGGGAAGAATCAATTTACAATGAGTTTGTTCAAAGGA
GTATTCAGTGGCCTAAGAAGTATGTTCTCGGAAATCCCCTGACCCCAGGAGTAAATCAAGGCCTTCAGGTTGATGAGGGA
CAATATGATAAAGCACTTGACCTCACTGAGAGTAGAAAGAAAGAAGGGTCCAAACTGGAATGTGGAGGAAACCTGTCCGG
GAATAAAGGTTGTATTATTCAGCCCACAGTTTTCTCTAATGTTAGAGATGAGATGCATATTGCCAAAGAGGAGATGTTTG
CAACTGTCCAGCAAATCATGAAATTTAAATTTTTAGATGATGTGATCAAAACAGCAAGC

Alignment

ORF - retro_lafr_1162 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.82 %
• Parental protein coverage: 63.77 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SMNAGKLFASSYMVDVGSSIKTLRYCAAWADKIQGRTIPIDGNFFTYTRHEPIGVCGQIIPWNFPLIMLI
          SMN.GKLF........G..IKT.RY....A.KIQG.TIPID.NFFTYTRH.PIG.CGQIIPWNF.L.ML.
Retrocopy SMNGGKLFGNLDLMGFGGCIKTSRYHVG*AEKIQGQTIPIDENFFTYTRHKPIGICGQIIPWNFLLVMLM

Parental  WKIGPALSCGNTVIVKPAEQTPLTALHVASLIKEAGFPPGVVNIVPGYGP-TAGAAISSHMDIDKVAFTG
          WKIGPAL.CGNT.IVKPA.QTPLTALHVASLIKEAGFPP.VVNIVPGY.P.T.GAAISSHMDI.KV.FTG
Retrocopy WKIGPAL-CGNTMIVKPATQTPLTALHVASLIKEAGFPPRVVNIVPGYRP<TTGAAISSHMDIKKVTFTG

Parental  STEVGKMIKEAAGKSNLKRVTLELGGKSPCIVFADADLDSAVEFAHQGVFFHQGQMCVAASRL-FVEESI
          S.EVGKM.KEA..KSNLKRVTLELGGK.PCIVFAD.DLD.AV.FA.QG..F.....C..A....F.EESI
Retrocopy SMEVGKMLKEAVEKSNLKRVTLELGGKTPCIVFADGDLDYAVAFARQGL-FYHQGQCCIAVSR>FWEESI

Parental  YDEFVRRSIERTKKYVFGNPLTPGVNQGPQIDKEQYDKILDLIESGKKEGAKLECGGGPWGNKGYFIQPT
          Y.EFV.RSI...KKYV.GNPLTPGVNQG.Q.D..QYDK.LDL.ES.KKEG.KLECGG...GNKG..IQPT
Retrocopy YNEFVQRSIQWPKKYVLGNPLTPGVNQGLQVDEGQYDKALDLTESRKKEGSKLECGGNLSGNKGCIIQPT

Parental  VFSNVTDEMRIAKEEIFGPVQQIMKFKSLDDVIKRAN
          VFSNV.DEM.IAKEE.F..VQQIMKFK.LDDVIK.A.
Retrocopy VFSNVRDEMHIAKEEMFATVQQIMKFKFLDDVIKTAS

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_1162 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 3 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000031532	1 retrocopy	retro_lafr_1162 ,
Macropus eugenii	ENSMEUG00000008847	1 retrocopy	retro_meug_354,
Tupaia belangeri	ENSTBEG00000001455	7 retrocopies	retro_tbel_2156, retro_tbel_2326, retro_tbel_3836, retro_tbel_3843, retro_tbel_3945, retro_tbel_3951, retro_tbel_4329,