RetrogeneDB ID: retro_lafr_1150

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_79:722325..723336(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CTSB
• Ensembl ID: ENSLAFG00000007380
• Aliases: None
• Description: None

Sequence

>retro_lafr_1150
TGGCAGCTCTTGGCTACCCTCTGCTGCCTGGTGGTGCTGACCAACACCCACAGCAGGCTGTATTTCAAGCCCCTATCAGA
TGAGCTCTTCAACCATGTCAACAAACATATACTACATGGCAGACTGGACACAACTTCCACAACGTGGGTGTGAGCTATGT
GAAGAGGCTGTGTGGGACCCTACTGAATGGACCCAAGCTGCCCCAGAGAGTTTTTTTTGCTGAGGAAATTGATCTGCCTG
AAAACTTTTCACGCTCGGGAAAACTGGTCAAAATGTGCAACCTTCAAAGAGATCAGAGACCAGGGTTCCTGTGGCTCTTG
CTGGGCATTTGGGGCTGTGGAGGCCATTTCTGACCGGGTCTGCATTCACACCAATGGGAATAGCAATGTGGAAGTGTCTG
TGGAGGCCTTGCTCACCTGCTGTCGCACGGAGTGTGGGGGCGGCTGCAGTGGGGGCTTTCCCGCTGGAGCTCGGAGCTTC
TGGACCAGGGAAGGCCTGGTTTCCGGTGGCCTCTATGACTCCCATGTAAGCTGCAGACCCTACTCCATCCCTCCATGTGA
GTACCACATCAGTGGCTCCCGGCCCCCCATGCAAGGGAGAAGGAGGAGAGACTCCCGAATGCAGCAAGCCCTGCGCACCT
GGCTATTCCCCATCTTACAAAGAAAACAAGCACTACGGATATAGTTCCCACGGTGTCTCTTCTTCTGAGATCATGGCTGA
AATCTACAAAAATGGCCCAGTAGAGGGCGCCTTTTCTGTGTATACAGACTTCTGGCGTACAAGTCTGGACTGTACCAGCA
TGTGACTGGAGAAGAGGTGGGAGGCCATGCCATCGGCATCCTGGGCTGAGGAGTGGAGAATGGCACCCCCTACTGGCTGG
CTGCCAACTCCTGGAACACTGACTGGGATGACAACGGCTTCTTTAAAATCCTCAGAGGACAGGATCACTGCAGAATCGAA
TCAGAAATTGTGGCTGGAATCCCAGACACTGACCAATACTGGAAAAAGGTC

Alignment

ORF - retro_lafr_1150 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.48 %
• Parental protein coverage: 99.71 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  WQLLATLCCLVVLTSAQSRLYFKPLSDELVNHVNK-LNTTWQAGHNFYDVDMSYVKRLCGTLLNGPKLPQ
          WQLLATLCCLVVLT...SRLYFKPLSDEL.NHVNK...TTWQ.GHNF..V..SYVKRLCGTLLNGPKLPQ
Retrocopy WQLLATLCCLVVLTNTHSRLYFKPLSDELFNHVNK<TYTTWQTGHNFHNVGVSYVKRLCGTLLNGPKLPQ

Parental  RVHLAEEMDLPENFD-ARENWPNCPTIKEIRDQGSCGSCWAFGAVEAISDRVCIHTNGNVNVEVSAEDLL
          RV..AEE.DLPENF..ARENW..C.T.KEIRDQGSCGSCWAFGAVEAISDRVCIHTNGN.NVEVS.E.LL
Retrocopy RVFFAEEIDLPENFS>ARENWSKCATFKEIRDQGSCGSCWAFGAVEAISDRVCIHTNGNSNVEVSVEALL

Parental  TCCHMECGDGCNGGFPAGAWNFWTKKGLVSGGLYDSHSQIGCRPYSIPPCEHHVNGSR-PPCKGEGGETP
          TCC..ECG.GC.GGFPAGA..FWT..GLVSGGLYDSH....CRPYSIPPCE.H..GSR.PPCKGEGGETP
Retrocopy TCCRTECGGGCSGGFPAGARSFWTREGLVSGGLYDSH--VSCRPYSIPPCEYHISGSR>PPCKGEGGETP

Parental  KCSKTCEPGYSPSYKEDKHYGYSSYGVPSSEQEIMAEIYKNGPVEGAFSVYTDF-LVYKSGVYQHVTGEE
          .CSK.C.PGYSPSYKE.KHYGYSS.GV.SS..EIMAEIYKNGPVEGAFSVYTDF.L.YKSG.YQHVTGEE
Retrocopy ECSKPCAPGYSPSYKENKHYGYSSHGVSSS--EIMAEIYKNGPVEGAFSVYTDF<LAYKSGLYQHVTGEE

Parental  VGGHAIRILGWGVENGTPYWLAANSWNTDWGDNGFFKILRGQDHCGIESEIVAGIPRTDQYWKKI
          VGGHAI.ILG.GVENGTPYWLAANSWNTDW.DNGFFKILRGQDHC.IESEIVAGIP.TDQYWKK.
Retrocopy VGGHAIGILG*GVENGTPYWLAANSWNTDWDDNGFFKILRGQDHCRIESEIVAGIPDTDQYWKKV

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_1150 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 4 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000164733	1 retrocopy	retro_hsap_3032,
Loxodonta africana	ENSLAFG00000007380	1 retrocopy	retro_lafr_1150 ,
Monodelphis domestica	ENSMODG00000012029	6 retrocopies	retro_mdom_1066, retro_mdom_1067, retro_mdom_1199, retro_mdom_1707, retro_mdom_1973, retro_mdom_1985,
Mus musculus	ENSMUSG00000021939	1 retrocopy	retro_mmus_1921,