RetrogeneDB ID: retro_psin_61

Retrocopy location

• Organism: Chinese softshell turtle (Pelodiscus sinensis)
• Coordinates: JH211925.1:77742..78360(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM30A
• Ensembl ID: ENSPSIG00000007174
• Aliases: None
• Description: transmembrane protein 30A [Source:HGNC Symbol;Acc:16667]

Sequence

>retro_psin_61
CTGACACACCCAGCCACGGAGTGCAGCCCCTTCCGCACTGACCCGCAGGGCATCCCCATCGCCCCCTGCGGGGCCATTGC
CAACAGCCTCTTCAATGACGCCTTCACCCTCTACCACGTTATCAATGGCTCCTTCTACCCTGTGCCCCTGGACAAAAGGG
GCATCTCCTGGTGGACCGACTCCAACGTGAAGTTCAGCAATCCAGAACCGGTCGATGGCACCCTGGAGAATGCCTTCAAG
AACACAACCAAGCCCCCCAATTGGCCCCGTGCTGCCTACCAGCTGGACCCAGACAACCCCAACAACACCGGTTTTATCAA
CGAGGACTTCATCGTGTGGATGCGTACTGCTGCCTTGCCCACGTTCCGCAAGCTCTACCGCCGTGTGCATGAAGGCAACT
TCTCCTCTGGCCTGCCCCAAGGCACCTACTGCCTCAACATCACCTACAACTACCCTGTCCTCTCCTTCCAGGGCACAAAG
AAGGTCATCTTCAGCACTGTTTCCTGGATGGGTGGCAAGAACCCCTTCCTGGGCATTGTCTATCTGGTCTTTGGCTCTGC
CTGCATCCTCACTGGCTTTGTCATGCTGGCTGTTCATATCAAGTACCAGAAACAAAAT

Alignment

ORF - retro_psin_61 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.45 %
• Parental protein coverage: 53.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLNPSKECEPYRTS-EGKPIAPCGAIANSMFNDTLELFRIDNETRIPVVLNKKGIAWWTDKNVKFRNPSG
          L..P..EC.P.RT...G.PIAPCGAIANS.FND...L....N....PV.L.K.GI.WWTD.NVKF.NP..
Retrocopy LTHPATECSPFRTDPQGIPIAPCGAIANSLFNDAFTLYHVINGSFYPVPLDKRGISWWTDSNVKFSNPEP

Parental  NAHNLTALFQGTTKPVNWPKPVYMLDSEADNN-GFINEDFIVWMRTAALPTFRKLYRLIERENNLQPTLQ
          ....L...F..TTKP.NWP...Y.LD....NN.GFINEDFIVWMRTAALPTFRKLYR....E.N....L.
Retrocopy VDGTLENAFKNTTKPPNWPRAAYQLDPDNPNNTGFINEDFIVWMRTAALPTFRKLYRRV-HEGNFSSGLP

Parental  AGKYSLDITYNYPVHSFDGRKRMILSTISWMGGKNPFLGIAYITVGSICFFLGVVLLVIHHKYGNRN
          .G.Y.L.ITYNYPV.SF.G.K..I.ST.SWMGGKNPFLGI.Y...GS.C...G.V.L..H.KY...N
Retrocopy QGTYCLNITYNYPVLSFQGTKKVIFSTVSWMGGKNPFLGIVYLVFGSACILTGFVMLAVHIKYQKQN

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_61 retrocopy.

TSS

Pelodiscus sinensis was not studied using FANTOM5 data.

Lab

retro_psin_61 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.

---

Parental genes homology:

Parental genes homology involve 15 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005100	1 retrocopy	retro_btau_72,
Canis familiaris	ENSCAFG00000002708	1 retrocopy	retro_cfam_26,
Callithrix jacchus	ENSCJAG00000010325	1 retrocopy	retro_cjac_801,
Cavia porcellus	ENSCPOG00000020712	1 retrocopy	retro_cpor_23,
Homo sapiens	ENSG00000112697	1 retrocopy	retro_hsap_12,
Myotis lucifugus	ENSMLUG00000011923	1 retrocopy	retro_mluc_1871,
Monodelphis domestica	ENSMODG00000018502	1 retrocopy	retro_mdom_287,
Mus musculus	ENSMUSG00000032328	1 retrocopy	retro_mmus_108,
Nomascus leucogenys	ENSNLEG00000004962	1 retrocopy	retro_nleu_69,
Otolemur garnettii	ENSOGAG00000015718	1 retrocopy	retro_ogar_22,
Pongo abelii	ENSPPYG00000016782	1 retrocopy	retro_pabe_204,
Pelodiscus sinensis	ENSPSIG00000007174	1 retrocopy	retro_psin_61 ,
Rattus norvegicus	ENSRNOG00000010895	1 retrocopy	retro_rnor_399,
Ictidomys tridecemlineatus	ENSSTOG00000002543	1 retrocopy	retro_itri_50,
Tarsius syrichta	ENSTSYG00000008211	1 retrocopy	retro_tsyr_928,