RetrogeneDB ID: retro_ttru_1931

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_99190:20406..20930(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LRRC59
• Ensembl ID: ENSTTRG00000000207
• Aliases: None
• Description: leucine rich repeat containing 59 [Source:HGNC Symbol;Acc:28817]

Sequence

>retro_ttru_1931
TGCTTGGACGAGAAGCAGCATGAGCAGTGCGCCAACAGGGTGTTAGAGCACACGAAGGCGGTACAGCTCGATCAGGAGCG
AGAGAGGCAGCGGCAGCTGGAAATAGACCGCGAGGCCGAGAAGACGTTGGGAGGCCAAGCAGCGAGCTAAGGAGGCTCCG
GAGCGGAACTGCGGACGCGGGAGAAGGCGGAAGAGAAGGAGCGCCGGAGAAAGGAGTAGGACGCCCTCAAAGCAGCCAAC
CAGGAGCAGAAGGAACCTAAGAAGGAAACAGATCAAGCCCCGAAATCTAAGTCCGGCTCTCGGCCCCGGAAGCCACCACC
CGGGAACCACACTCAATCCTGGGCTGTGCTGGGGCTGCTGCTGCCACTGCTGTTGCGTGTGGTTGGCGGGCTCGTTGCTT
GTCGAGTGACGGAGCTGCAGCAGCAGCCCGTCTGCACCAGTGTGAACACCATCTACGACAACGCGCTCTGGCGCTGCGCA
GCCACGGCATCCTCCAGTGGGTCCTGCAGACCGATTCTCAGCAG

Alignment

ORF - retro_ttru_1931 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80. %
• Parental protein coverage: 57.65 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  CLDEKQCKQCANKVLQHMKAVQVDQERERQRRLEIDREAEK-KWEAKQRAKEAQER-ELRKREKAEEKER
          CLDEKQ..QCAN.VL.H.KAVQ.DQERERQR.LEIDREAEK..WEAKQRAKEA.ER.ELR.REKAEEKER
Retrocopy CLDEKQHEQCANRVLEHTKAVQLDQERERQRQLEIDREAEK>RWEAKQRAKEAPER<ELRTREKAEEKER

Parental  RRKEYDALKAAKREQEKKPKKEANQAPKSKSGSRPRKAAPRKHTRSWAVLRLLLLLLLLCVAGGLVACRV
          RRKE.DALKAA..EQ.K.PKKE..QAPKSKSGSRPRK..P..HT.SWAVL.LLL.LLL..V.GGLVACRV
Retrocopy RRKE*DALKAANQEQ-KEPKKETDQAPKSKSGSRPRKPPPGNHTQSWAVLGLLLPLLLR-VVGGLVACRV

Parental  TELQQQPLCTSVNTIYDSAL-RGLRSHDILRWVLQTDSQQ
          TELQQQP.CTSVNTIYD.AL...LRSH.IL.WVLQTDSQQ
Retrocopy TELQQQPVCTSVNTIYDNAL<LALRSHGILQWVLQTDSQQ

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tursiops truncatus was not studied using RNA-Seq expression data.

ChIP-Seq

Tursiops truncatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ttru_1931 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1931 was not experimentally validated.

Homology

Retrocopy orthology:

Tursiops truncatus 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 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018827	1 retrocopy	retro_cjac_2342,
Equus caballus	ENSECAG00000018072	1 retrocopy	retro_ecab_240,
Homo sapiens	ENSG00000108829	1 retrocopy	retro_hsap_3479,
Gorilla gorilla	ENSGGOG00000006310	1 retrocopy	retro_ggor_2346,
Monodelphis domestica	ENSMODG00000020901	1 retrocopy	retro_mdom_1882,
Nomascus leucogenys	ENSNLEG00000009066	1 retrocopy	retro_nleu_2629,
Pongo abelii	ENSPPYG00000008284	3 retrocopies	retro_pabe_2687, retro_pabe_2874, retro_pabe_2875,
Pan troglodytes	ENSPTRG00000009398	1 retrocopy	retro_ptro_2985,
Tarsius syrichta	ENSTSYG00000000371	1 retrocopy	retro_tsyr_25,
Tursiops truncatus	ENSTTRG00000000207	1 retrocopy	retro_ttru_1931 ,