RetrogeneDB ID: retro_ttru_1702

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_86709:148..612(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NIPSNAP3A
• Ensembl ID: ENSTTRG00000012307
• Aliases: None
• Description: nipsnap homolog 3A (C. elegans) [Source:HGNC Symbol;Acc:23619]

Sequence

>retro_ttru_1702
AGTTTTGCTCCTTGAGCTGAAGTTCAGAAAGGCTCGGCCAAGAATAAAGAATGCCCAGAACAATTTCTTATTCCAAATTT
GGCTCTCATTGACAAGCAAGAGTTTGAGATTATTTATGGGGTACCATAGTGCAAACTAGAAAAAAAAAATCCCAAAGGAG
TCTATGAGCCAGTTATTTTCCAGATGAAGCCTGCTGGGCCAGCTCTGTGGGGTGATGAGTTTAAAACGGTGGTGGATGCC
CATGTTGATTTAGGCTACACAGAATTGGTTGGCGTTCTCCACCCAGAATACAGAGCACCCAGCAGAGTTCATGTTCTTTG
GTGAAATGAGAGTGCAGATATTCATGCAGCTGGGGGACATCAGTCTCATGAGGATCTCACACTTGTGGTCACTGGGAAAA
TGTCAACTACCAAGTGTCACAGCAAAGTTTGCTTCTGATTCCTATGTCATTTTTACCGTTGAAA

Alignment

ORF - retro_ttru_1702 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.51 %
• Parental protein coverage: 55.12 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NFAHRTEVQKALAKDKEWQEQFLIPNLALIDKQESEITYLVPWCKLEKPPKEGVYELATFQMKPGGPALW
          .FA...EVQK..AK.KE..EQFLIPNLALIDKQE.EI.Y.VP.CKL......GVYE...FQMKP.GPALW
Retrocopy SFAP*AEVQKGSAKNKECPEQFLIPNLALIDKQEFEIIYGVP*CKLXXXXPKGVYEPVIFQMKPAGPALW

Parental  GDPFKRAVHTHVNQGYTKLVGVFHAEYGILNRVHVLWWNESADSRAAGRHQSHEDPRVVAAVRESVN-FL
          GD.FK..V..HV..GYT.LVGV.H.EY....RVHVLW.NESAD..AAG.HQSHED...V.....S.....
Retrocopy GDEFKTVVDAHVDLGYTELVGVLHPEYRAPSRVHVLW*NESADIHAAGGHQSHEDLTLVVTGKMSTT<QV

Parental  GSQQNMLLIPMSFSPLK
          ..Q...L..PMSF.PLK
Retrocopy SQQSLLLI-PMSFLPLK

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_1702 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1702 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014253	1 retrocopy	retro_acar_133,
Canis familiaris	ENSCAFG00000023949	1 retrocopy	retro_cfam_295,
Cavia porcellus	ENSCPOG00000009373	1 retrocopy	retro_cpor_690,
Dasypus novemcinctus	ENSDNOG00000000943	1 retrocopy	retro_dnov_482,
Echinops telfairi	ENSETEG00000016120	1 retrocopy	retro_etel_1335,
Myotis lucifugus	ENSMLUG00000010147	1 retrocopy	retro_mluc_924,
Oryctolagus cuniculus	ENSOCUG00000007880	1 retrocopy	retro_ocun_1385,
Tursiops truncatus	ENSTTRG00000012307	1 retrocopy	retro_ttru_1702 ,