RetrogeneDB ID: retro_ttru_1882

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_97036:175373..176388(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SHMT2
• Ensembl ID: ENSTTRG00000013079
• Aliases: None
• Description: serine hydroxymethyltransferase 2 (mitochondrial) [Source:HGNC Symbol;Acc:10852]

Sequence

>retro_ttru_1882
ATGTTGCCCTTCTCTTTGCTCTGGGCGACTTGGCCTCAGCAGAGATGTGGTCACCTGGTCAGCATGGCCATAAGGTGCCA
GCACAGCGAGGCGGCCCAGACCCAGACTGGAAAAGCAACCAAGGGCTGGTCAGGCCAGGAGAGTCTATCAGACAGTGGCC
CTGAGATACGGGAGCTGCTACGGAGAGAGAAGGACAGGCAGTGTCGCGGCCTGGAAGCTCACTGCTCCAGGGAACTTCTG
CAGCCGAGCTGCGCCGGAGGCCCTGGGGTCCTGTCTGAGCAGCAAGTACTCGGAGGGTTATCCTGGCAAGAGGTACTATG
GAGGAGCAGAGGCAGTGGATGAAATCGAGCTGCTGTGTCAGCGCCGGGCCTTGGAGGCCTTTGACCTGGATCCTGCTCAG
TGGGGAGTCAATGTCCAGCCCTACTCGGGGTCCCCAGCCAACCTGGCTGCCTACACAGCCCTTCTGCAGCCTCATGACCA
AATCATGGGGGGACCCCGTGCCCGATGGGGGCCATCTCACCCATGGCTACATGTCTGATGTCAAGCGGATCTCAGCCACA
TCCATCTTCTTCAAGTCTACGTCCTATAAGCTGCAACCCAAAACCAGCCTCACTGACTATGACCAGCCGGCACTTGCTGC
TCGGCTCTTCCGACCTTGACTCATCAGAGCTGGTACCGGTGCCTATGCTCGCCTCATCGACTACGCCCGCATGAGAGAGG
TGTGTGACGAGGTCAAGGCGCACCTGCTGGCAGACGTGGCCCACATCAGTGGCCTGGTGGCTGCCAAGGTGATCCCCTCA
CCTTTCAAGCATGTGGATGTTGTCGCCACTACCACTCACAAGACCCTTCGAGGGGCCAGGTCAGGACTCCTCTTCTGCCG
GAAGGGGGTGCGGGCTGTGGACCCCAAGACTGGCCAGGATATCCTTCCACGTTTGAGGACCGAATCAACTTTGCTGTGTT
CCCATCCCTGCAGGGGGGCCCCCAGAACCATGCCATTGCTGCAGTGTCTGTGGCC

Alignment

ORF - retro_ttru_1882 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.34 %
• Parental protein coverage: 67.33 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MLPFSLLWATRPLRRCGRLVRMAIRCQHSEAAQTQSGEATKGWSGQESLSDSDPEMWELLRREKDRQCRG
          MLPFSLLWAT.P..RCG.LV.MAIRCQHSEAAQTQ.G.ATKGWSGQESLSDS.PE..ELLRREKDRQCRG
Retrocopy MLPFSLLWATWPQQRCGHLVSMAIRCQHSEAAQTQTGKATKGWSGQESLSDSGPEIRELLRREKDRQCRG

Parental  LE-LIASENFCSRAALEALGSCLNNKYSEGYPGKRYYGGTEVVDEIELLCQRRALEAFDLNPAQWGVNVQ
          LE.L.A..NFCSRAA.EALGSCL..KYSEGYPGKRYYGG.E.VDEIELLCQRRALEAFDL.PAQWGVNVQ
Retrocopy LE>LTAPGNFCSRAAPEALGSCLSSKYSEGYPGKRYYGGAEAVDEIELLCQRRALEAFDLDPAQWGVNVQ

Parental  PYSGSPANLAAYTALLQPHDRIMGLD-LPDGGHLTHGYMSDVKRISATSIFFESMPYKLNPKTGLIDYDQ
          PYSGSPANLAAYTALLQPHD.IMG....PDGGHLTHGYMSDVKRISATSIFF.S..YKL.PKT.L.DYDQ
Retrocopy PYSGSPANLAAYTALLQPHDQIMGGP>VPDGGHLTHGYMSDVKRISATSIFFKSTSYKLQPKTSLTDYDQ

Parental  LALTARLFRPRLIIAGTSAYARLIDYARMREVCDEVKAHLLADMAHISGLVAAKVIPSPFEHADVVTTTT
          .AL.ARLFRP.LI.AGT.AYARLIDYARMREVCDEVKAHLLAD.AHISGLVAAKVIPSPF.H.DVV.TTT
Retrocopy PALAARLFRP*LIRAGTGAYARLIDYARMREVCDEVKAHLLADVAHISGLVAAKVIPSPFKHVDVVATTT

Parental  HKTLRGARSRLIFYRKGVRAVDPKTGREI-PYTFEDRINFAVFPSLQGGSHNHAIAAVAVA
          HKTLRGARS.L.F.RKGVRAVDPKTG..I.P.TFEDRINFAVFPSLQGG..NHAIAAV.VA
Retrocopy HKTLRGARSGLLFCRKGVRAVDPKTGQDI<PSTFEDRINFAVFPSLQGGPQNHAIAAVSVA

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_1882 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1882 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000014334	2 retrocopies	retro_meug_77, retro_meug_993,
Tursiops truncatus	ENSTTRG00000013079	1 retrocopy	retro_ttru_1882 ,