RetrogeneDB ID: retro_ttru_1225

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_107606:7136..7611(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SAR1B
• Ensembl ID: ENSTTRG00000016864
• Aliases: None
• Description: SAR1 homolog B (S. cerevisiae) [Source:HGNC Symbol;Acc:10535]

Sequence

>retro_ttru_1225
TCCTTCATATTTGATTGGATATACAGTGGTTTCAGCAGAATGCTACAGTTTTTAGGATTATATAAGAGAACTGGCAAATT
GGTATTTCTTGGATTGGATAATGTGGGAAAAACAACATTGCTATATATGCTAAAAGATGACAGACTTGGACACATGTCCC
AATGTTATCTCCCCTTTCAAAAGAACTAACCATTACTGGCATGACCTTTGCAACTTTTGATCTGGGTAAACATGTTCAAG
ATCAAAGAGTGTGGAAAAACTACCTTCCTGCTATCAATGGCATTACAGTTCTGGTGGATTGTGCAGATCATAAAAGGCTG
TTAGAATCAAAAGAAGAACTTGATTCACTAATGACAGTTGAAACCATTTCTAATGTGTCTATACTGATTCTTGGGAATAA
GATCAACAGACCTGAAGCCATCAGTGAAGAGAGGTTACAAGAGATGTTGGTTTACACGGTCAGACAACAGGAAGG

Alignment

ORF - retro_ttru_1225 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.99 %
• Parental protein coverage: 80.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SFIFDWIYSGFSSVLQFLGLYKKTGKLVFLGLDNAGKTTLLHMLKDDRLGQ-HVPTLHPTSEELTIAGMT
          SFIFDWIYSGFS..LQFLGLYK.TGKLVFLGLDN.GKTTLL.MLKDDRLG..HVP.L.P.S.ELTI.GMT
Retrocopy SFIFDWIYSGFSRMLQFLGLYKRTGKLVFLGLDNVGKTTLLYMLKDDRLGH<HVPMLSPLSKELTITGMT

Parental  FTTFDLGGHVQARRVWKNYLPAINGIVFLVDCADHERLLESKEELDSLMTDETVANVPILILGNKIDRPE
          F.TFDLG.HVQ..RVWKNYLPAINGI..LVDCADH.RLLESKEELDSLMT.ET..NV.ILILGNKI.RPE
Retrocopy FATFDLGKHVQDQRVWKNYLPAINGITVLVDCADHKRLLESKEELDSLMTVETISNVSILILGNKINRPE

Parental  AISEERLREMF-GLYGQTTGK
          AISEERL.EM..GL.GQTTG.
Retrocopy AISEERLQEML<GLHGQTTGR

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_1225 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1225 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 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017849	1 retrocopy	retro_amel_1075,
Dasypus novemcinctus	ENSDNOG00000013784	3 retrocopies	retro_dnov_1584, retro_dnov_1804, retro_dnov_919,
Loxodonta africana	ENSLAFG00000001021	1 retrocopy	retro_lafr_1043,
Oryctolagus cuniculus	ENSOCUG00000008250	1 retrocopy	retro_ocun_1004,
Pteropus vampyrus	ENSPVAG00000012433	2 retrocopies	retro_pvam_1219, retro_pvam_725,
Tursiops truncatus	ENSTTRG00000016864	2 retrocopies	retro_ttru_1225 , retro_ttru_857,