RetrogeneDB ID: retro_psin_2

Retrocopy location

• Organism: Chinese softshell turtle (Pelodiscus sinensis)
• Coordinates: JH224670.1:488139..488892(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPSIG00000000212
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: YWHAQ
• Ensembl ID: ENSPSIG00000012692
• Aliases: None
• Description: tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide [Source:HGNC Symbol;Acc:12854]

Sequence

>retro_psin_2
ATGGCCAGAAACCAGCAGGTGCAGAAAGCCAAGCTGGCCGAGCAGGCGGAGCGCTATGAGAACATGGCAGATTTCATGAA
GGCCGTGGTGGAGCACGGGGACGAGCTCTCCAACGAGGAGCGCAACCTCCTCTCGGTGGCCTACAAGAACGTGGTGGGGT
GCCAGCGCTCTGCCTGGCGGGTCATCTCCAGCATCGAGCACAAGACTGAGGAGGGCGACGAGAAAACGCCGCTGGTGAGC
GAGTACCGCGAGAAGGTGGAGGGGGAGCTGAAGGACGTCTGCAATGTCGTTCTGGGGCTGCTGGACAAGCATCTCATTAA
GAAAGCCAGTGACCCAGAGAGCAAGGTCTTCTACCTGAAGATGAAGGGAGACTACTACCGCTACCTGGCCGAGGTAGCCA
CCGGGGATGACCGCAAGGAGACCATAGAAAACGCCCAGAAAGCTTACCAGGAAGCAATGGACATCAGCAAGAAGGAGATG
CAGCCCACCAACCCCATCCGCCTTGGGCTCGCCCTTAACTTCTCCGTCTTCCACTACGAGATCGCCAACGCCCCGGAGCA
GGCCATCACGCTGGCTAAAACCACGTTCGACGAAGCCATGGGCGACCTGCACACGCTCAGTGAAGACTCGTACAAGGACA
GCACCCTCATCATGCAGCTGCTCAGGGACAACCTTACGCTATGGACGGCGGAGTGCGCGGGAGAAGACGGCGGAGAAGCC
GGTGGAGAAGCCGGGGAAGAGCCTAAGAACTGA

Alignment

ORF - retro_psin_2 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.38 %
• Parental protein coverage: 98.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEKTEMIQKAKLAEQAERYDDMATCMKAVTEQGAELSNEERNLLSVAYKNVVGGRRSAWRVISSIEQKTD
          M......QKAKLAEQAERY..MA..MKAV.E.G.ELSNEERNLLSVAYKNVVG..RSAWRVISSIE.KT.
Retrocopy MARNQQVQKAKLAEQAERYENMADFMKAVVEHGDELSNEERNLLSVAYKNVVGCQRSAWRVISSIEHKTE

Parental  TNDKKMQLVKDYREKVESELRSICTTVLELLDKFLIANATNPESKVFYLKMKGDYFRYLAEVACGDDRKQ
          ..D.K..LV..YREKVE.EL...C..VL.LLDK.LI..A..PESKVFYLKMKGDY.RYLAEVA.GDDRK.
Retrocopy EGDEKTPLVSEYREKVEGELKDVCNVVLGLLDKHLIKKASDPESKVFYLKMKGDYYRYLAEVATGDDRKE

Parental  TIENSQAAYQEAFDISKKEMQPTHPIRLGLALNFSVFYYEILNNPELACTLAKTAFDEAIAELDTLNEDS
          TIEN.Q.AYQEA.DISKKEMQPT.PIRLGLALNFSVF.YEI.N.PE.A.TLAKT.FDEA...L.TL.EDS
Retrocopy TIENAQKAYQEAMDISKKEMQPTNPIRLGLALNFSVFHYEIANAPEQAITLAKTTFDEAMGDLHTLSEDS

Parental  YKDSTLIMQLLRDNLTLWTSDSAGEECDAAEG
          YKDSTLIMQLLRDNLTLWT...AGE....A.G
Retrocopy YKDSTLIMQLLRDNLTLWTAECAGEDGGEAGG

Legend:

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

Expression

RNA-Seq

Pelodiscus sinensis was not studied using RNA-Seq expression data.

ChIP-Seq

Pelodiscus sinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_psin_2 retrocopy.

TSS

Pelodiscus sinensis was not studied using FANTOM5 data.

Lab

retro_psin_2 was not experimentally validated.

Homology

Retrocopy orthology:

Pelodiscus sinensis 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 9 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006394	2 retrocopies	retro_cjac_2197, retro_cjac_3127,
Echinops telfairi	ENSETEG00000015359	4 retrocopies	retro_etel_1027, retro_etel_1048, retro_etel_235, retro_etel_65,
Macropus eugenii	ENSMEUG00000014442	7 retrocopies	retro_meug_1122, retro_meug_1208, retro_meug_1259, retro_meug_1549, retro_meug_1918, retro_meug_2106, retro_meug_538,
Monodelphis domestica	ENSMODG00000014740	1 retrocopy	retro_mdom_1339,
Nomascus leucogenys	ENSNLEG00000013534	3 retrocopies	retro_nleu_2543, retro_nleu_750, retro_nleu_869,
Pongo abelii	ENSPPYG00000012663	4 retrocopies	retro_pabe_1165, retro_pabe_2490, retro_pabe_3391, retro_pabe_3511,
Pelodiscus sinensis	ENSPSIG00000003703	1 retrocopy	retro_psin_13,
Pelodiscus sinensis	ENSPSIG00000012692	1 retrocopy	retro_psin_2 ,
Rattus norvegicus	ENSRNOG00000008104	5 retrocopies	retro_rnor_1569, retro_rnor_2065, retro_rnor_2123, retro_rnor_2180, retro_rnor_2746,