RetrogeneDB ID: retro_lafr_878

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_43:8603385..8603866(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNRPC
• Ensembl ID: ENSLAFG00000013534
• Aliases: None
• Description: U1 small nuclear ribonucleoprotein C [Source:UniProtKB/TrEMBL;Acc:G3TBG7]

Sequence

>retro_lafr_878
ATACCCAAGTTTTATTATGACTGCTGTGATACATACCTGACTCTCACCCATGACTCGCCATCTGTGAGAAAGACATACTG
CAGTGATAGGAAACACAAAGAGAATGTGAATGACTACTATCAGAAATGGATGGAAGAGCAAGCTCAGAGCCTGATTAACA
AAGTAACAGTTGCATTGCAATACCGAAAGATACCTCCTACTCCATTCTCTGCTCCTCCTCCAGCAAGGGTGATGATCCTG
CCTCCTCTCAGTCTATTGGGTCCTCCTTGCCCTGGTACGATACCAGTAGCCCATATGAGGTGCCTTCCCATGATCCAATG
ATGGGCCCTCCTTCTCCTAGGATGATGTCAGTGGGATCTGCTCATGGAATAGGCCCCCCATGAGAGGCCACATGCCATTA
ATGCCTGGGACTCCAATGATGAGGCATCTCTCCTGTCCCATGACAGTGCCTACTCAGCCAGGAATGACCTGAGCAGACAG
A

Alignment

ORF - retro_lafr_878 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.17 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPKFYCDYCDTYLT--HDSPSVRKTHCSGRKHKENVKDYYQKWMEEQAQSLIDKTTAAFQQGKIPPTPFS
          .PKFY.D.CDTYLT..HDSPSVRKT.CS.RKHKENV.DYYQKWMEEQAQSLI.K.T.A.Q..KIPPTPFS
Retrocopy IPKFYYDCCDTYLTLTHDSPSVRKTYCSDRKHKENVNDYYQKWMEEQAQSLINKVTVALQYRKIPPTPFS

Parental  APPPAGAMIPPPPSLPGPPRPGMMPAPHMGGPPMM-PMMGPPPPGMMPVGPAPGM-RPPMGGHMPMMPGP
          APPPA..MI.PP.SL.GPP.PG..P..HM...PM..PMMGPP.P.MM.VG.A.G..RPPM.GHMP.MPG.
Retrocopy APPPARVMILPPLSLLGPPCPGTIPVAHMRCLPMI<PMMGPPSPRMMSVGSAHGI<RPPMRGHMPLMPGT

Parental  PMMRPPARPMMVPTRPGMTRPDR
          PMMR....PM.VPT.PGMT..DR
Retrocopy PMMRHLSCPMTVPTQPGMT*ADR

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_878 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 11 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000024549	1 retrocopy	retro_btau_1636,
Canis familiaris	ENSCAFG00000001231	3 retrocopies	retro_cfam_348, retro_cfam_402, retro_cfam_409,
Callithrix jacchus	ENSCJAG00000015321	16 retrocopies	retro_cjac_1009, retro_cjac_1015, retro_cjac_1064, retro_cjac_1750, retro_cjac_1937, retro_cjac_2014, retro_cjac_2395, retro_cjac_2456, retro_cjac_2785, retro_cjac_3056, retro_cjac_3110, retro_cjac_400, retro_cjac_4010, retro_cjac_617, retro_cjac_770, retro_cjac_873,
Homo sapiens	ENSG00000124562	6 retrocopies	retro_hsap_1531, retro_hsap_1866, retro_hsap_2865, retro_hsap_3195, retro_hsap_3829, retro_hsap_4241,
Loxodonta africana	ENSLAFG00000013534	2 retrocopies	retro_lafr_621, retro_lafr_878 ,
Monodelphis domestica	ENSMODG00000013904	1 retrocopy	retro_mdom_22,
Nomascus leucogenys	ENSNLEG00000008392	2 retrocopies	retro_nleu_2129, retro_nleu_99,
Oryctolagus cuniculus	ENSOCUG00000026668	3 retrocopies	retro_ocun_1019, retro_ocun_184, retro_ocun_196,
Otolemur garnettii	ENSOGAG00000008755	9 retrocopies	retro_ogar_1040, retro_ogar_130, retro_ogar_1763, retro_ogar_183, retro_ogar_2434, retro_ogar_3064, retro_ogar_3322, retro_ogar_3377, retro_ogar_697,
Pongo abelii	ENSPPYG00000017272	4 retrocopies	retro_pabe_1271, retro_pabe_3066, retro_pabe_3225, retro_pabe_915,
Sarcophilus harrisii	ENSSHAG00000000945	1 retrocopy	retro_shar_112,