RetrogeneDB ID: retro_ttru_1550

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_115994:24312..24997(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MDH2
• Ensembl ID: ENSTTRG00000014834
• Aliases: None
• Description: malate dehydrogenase 2, NAD (mitochondrial) [Source:HGNC Symbol;Acc:6971]

Sequence

>retro_ttru_1550
ATGACACGGGACGACCTACTCAACACCCACGCTACAATCCTGGCCACCCTGACTGCTGCCTGTGCCCGCACAGCCCCGAG
ACCATGATCTGCGTCATTTCAAATCCAGTTAACTCCACCATCCCAATCACAGCAGAAGTTTTCAAGAAACATGGAGTTTA
CAACCCCAGTAAAATCTTTGGGGTGACAACCCTGGACATTGTCCAAGCCAACACTTTTGCTGCCGATCTAAAGGGTGTGG
ACCGGCTCGAGTCAACGTTCTTGTCATTGGCGGCCATGCTGGGAGGATCATCCCCCTGATCTCAGTGCACCCCCAAAGTG
GACTTTCCCCAGGACCTGCTGACTACCCACACCGGGTGGATCCAGGAGGCTGGCACGGAGGTGGGCAAGGCTAAGGCCAC
AACAAACCCTGCCACCCTGTCCACCGTGTACGCCGGAGCCCGCCGATTTGTCTTCTCCCTCGTGGATGCGATGAACTGAA
AAGCTGTCGAATGTTCCCTCGTCAAGTCCCAAGAAAACAGACCGTCTATATTTCTCCACACCGTCGATGCTGGGGTGAAA
GGGCATCGAGAAGAATCTAGGCATCGGCAAAATCTCCCCCGTTTGAAGAGAAGGTGATTGCCAAGGCCATTTCTGAGCTG
AAAGCCTCCATCAAGAAACGAGAGGAGTTTGTAAAAAACATGAAA

Alignment

ORF - retro_ttru_1550 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.73 %
• Parental protein coverage: 68.34 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MTRDDLFNTNATIVATLTAACAQ-HCPEAMICIIANPVNSTIPITAEVFKKHGVYNPSKIFGVTTLDIVR
          MTRDDL.NT.ATI.ATLTAACA..H.PE.MIC.I.NPVNSTIPITAEVFKKHGVYNPSKIFGVTTLDIV.
Retrocopy MTRDDLLNTHATILATLTAACAR<HSPETMICVISNPVNSTIPITAEVFKKHGVYNPSKIFGVTTLDIVQ

Parental  ANTFVAELKGLD-PARVSVPVIGGHAGKTIIPLVS-QCTPK-VDFPQDQLTPLIGRIQEAGTEVVKAKAG
          ANTF.A.LKG.D.PARV.V.VIGGHAG..IIPL.S....PK.VDFPQD.LT...G.IQEAGTEV.KAKA.
Retrocopy ANTFAADLKGVD<PARVNVLVIGGHAGR-IIPLIS<SAPPK<VDFPQDLLTTHTGWIQEAGTEVGKAKAT

Parental  AGSATLSMAYAGA-RFVFSLVDAMNGKEGVVECSFVKSQE-TDCPYFSTPLLLGKKGIEKNLGIGKIS-P
          ...ATLS..YAGA.RFVFSLVDAMN.K...VECS.VKSQE.TD..YFSTP..LG.KGIEKNLGIGKIS.P
Retrocopy TNPATLSTVYAGARRFVFSLVDAMN*K--AVECSLVKSQE>TDRLYFSTPSMLG*KGIEKNLGIGKIS>P

Parental  FEEKMIAEAIPELKASIKKGEEFVKNMK
          FEEK.IA.AI.ELKASIKK.EEFVKNMK
Retrocopy FEEKVIAKAISELKASIKKREEFVKNMK

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_1550 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1550 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
Ailuropoda melanoleuca	ENSAMEG00000010846	1 retrocopy	retro_amel_361,
Canis familiaris	ENSCAFG00000013515	2 retrocopies	retro_cfam_182, retro_cfam_41,
Myotis lucifugus	ENSMLUG00000017795	1 retrocopy	retro_mluc_1948,
Monodelphis domestica	ENSMODG00000013680	1 retrocopy	retro_mdom_1711,
Mus musculus	ENSMUSG00000019179	1 retrocopy	retro_mmus_2451,
Otolemur garnettii	ENSOGAG00000009705	1 retrocopy	retro_ogar_3068,
Pteropus vampyrus	ENSPVAG00000003397	1 retrocopy	retro_pvam_981,
Tupaia belangeri	ENSTBEG00000003190	1 retrocopy	retro_tbel_440,
Tursiops truncatus	ENSTTRG00000014834	1 retrocopy	retro_ttru_1550 ,
Drosophila melanogaster	FBgn0262559	2 retrocopies	retro_dmel_54, retro_dmel_76,