RetrogeneDB ID: retro_lafr_84

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_56:3077481..3077931(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000021905
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLAFG00000006089
• Aliases: None
• Description: Stathmin [Source:UniProtKB/TrEMBL;Acc:G3SXG9]

Sequence

>retro_lafr_84
AGGGCTTCTTCTGATATCCAGGTGAAAGAACTGGAGAAGCGGGCCTCAGGCCAGGCCTTTGAGCTGATACTCAGCCCTCG
TTCAAAAGAGTCTGTCCCAGAATTCCCCCTTTCCCCTCCGAAGAAGAAGGACCTTTCCCTGGAGGAAATTCAGAAGAAAT
TAGAAGCTGCTGAAGAAAGACGCAAGTCTCATGAAGCTGAGGTCTTGAAGCAGCTTGCTGAGAAACGAGAGCACGAGAAA
GAAGTGCTTCAGAAAGCAATAGAAGAGAACAACAACTTCAGTAAAATGGCGGAAGAGAAACTGACCCACAAAATGGAAGC
CAACAAAGAGAACCGAGAGGCACAGATGGCTGCCAAACTGGAGCGTTTGCGAGAAAAGGACAAGCACATTGAAGAAGTGC
GGAAGAACAAAGAATCCAAAGATCCTGCTAATGAGGCTGAAGCTGACTAA

Alignment

ORF - retro_lafr_84 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.65 %
• Parental protein coverage: 99.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ASSDIQVKELEKRASGQAFELILSPRSKEAVPEFPLSPPKKKDLSLEEIQKKLEAAEERRKSHEAEVLKQ
          ASSDIQVKELEKRASGQAFELILSPRSKE.VPEFPLSPPKKKDLSLEEIQKKLEAAEERRKSHEAEVLKQ
Retrocopy ASSDIQVKELEKRASGQAFELILSPRSKESVPEFPLSPPKKKDLSLEEIQKKLEAAEERRKSHEAEVLKQ

Parental  LAEKREHEKEVLQKAIEENNNFSKMAEEKLTHKMEANKENREAQMAAKLERLREKDKHIEEVRKNKESKD
          LAEKREHEKEVLQKAIEENNNFSKMAEEKLTHKMEANKENREAQMAAKLERLREKDKHIEEVRKNKESKD
Retrocopy LAEKREHEKEVLQKAIEENNNFSKMAEEKLTHKMEANKENREAQMAAKLERLREKDKHIEEVRKNKESKD

Parental  PADEAEAD
          PA.EAEAD
Retrocopy PANEAEAD

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_84 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.

---

Parental genes homology:

Parental genes homology involve 13 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013761	1 retrocopy	retro_btau_247,
Callithrix jacchus	ENSCJAG00000009462	2 retrocopies	retro_cjac_3206, retro_cjac_474,
Cavia porcellus	ENSCPOG00000011075	1 retrocopy	retro_cpor_1505,
Equus caballus	ENSECAG00000021662	1 retrocopy	retro_ecab_490,
Loxodonta africana	ENSLAFG00000006089	1 retrocopy	retro_lafr_84 ,
Mustela putorius furo	ENSMPUG00000015774	1 retrocopy	retro_mputfur_1191,
Mus musculus	ENSMUSG00000028832	3 retrocopies	retro_mmus_1660, retro_mmus_2470, retro_mmus_3383,
Oryctolagus cuniculus	ENSOCUG00000006493	1 retrocopy	retro_ocun_56,
Pteropus vampyrus	ENSPVAG00000006344	1 retrocopy	retro_pvam_53,
Rattus norvegicus	ENSRNOG00000016810	4 retrocopies	retro_rnor_1604, retro_rnor_1855, retro_rnor_2048, retro_rnor_765,
Sorex araneus	ENSSARG00000011057	2 retrocopies	retro_sara_271, retro_sara_764,
Sarcophilus harrisii	ENSSHAG00000006382	1 retrocopy	retro_shar_391,
Ictidomys tridecemlineatus	ENSSTOG00000021708	5 retrocopies	retro_itri_1806, retro_itri_1833, retro_itri_554, retro_itri_819, retro_itri_826,