RetrogeneDB ID: retro_psin_22

Retrocopy location

• Organism: Chinese softshell turtle (Pelodiscus sinensis)
• Coordinates: JH211792.1:5351647..5352595(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPSIG00000000502
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: EPCAM
• Ensembl ID: ENSPSIG00000015680
• Aliases: None
• Description: epithelial cell adhesion molecule [Source:HGNC Symbol;Acc:11529]

Sequence

>retro_psin_22
CTTTCTCCCTTGAACATGGAATCTAGATTTGGAGTTGTGCTGGTTTTAATCTTGGCAGCTGCATCATCATCTGCCCAGAA
GGCCTGTACCTGTGCAACCAACAGACGGACCCAATGCAGTGAAGACATATCTGGGAACTGCCTCTGCAGGTCGGTGGGTT
CAAATCAAAGAGTGGATTGTTCAGTGTTGACTTCAAAATGCCTCTTGATGAAGGCAGAAATGAGCCCCTCGAAGGCCAGG
CGCTTCTCCAAACCTGAGCTGGGCTTTCTAGACAATGATGGAATTTACAATCCGGACTGTGAGGACAGTGGTATCTTCAA
AGCCAGGCAGTGCAATCAGACTGACACTTGCTGGTGCGTGAACACTGCTGGTGTGAGAAGAACTGATAAGGGTGACAAAA
ACCTGAGGTGCAGTGAACTAGTCAGAACTAACTGGATCTTCCTTGAACTGAAACACAAGGAGAGGTCGGAACCTTTCCAG
GCTGCTGAAGTTGCCAGTGGACTGAGGCAGATAATTCAGAACAGATACAAGCTGCATCCAAAGTACATCACTGCCATTGA
GTATGAATACCCATTCATCCATATTGACCTGAAACAAAATGCTTCCCAGAAATCCAGGGGAGATGTCGATATAGCTGATG
TGGCTTATTACTTTGAAAAAGATGTTAAAGGTGACTCCATATTTGATCCTAGTAATGCATTCAACCTCTCTGTTAGCGGA
CAGCCTCTGGATGTGGAAGGAATTTTAATTTACTATGTGGATGAAAAGCCACCTGAATTTTCTATGAAACGTCTGACTGC
TGGCGTTATTGCTGTGTTGGCAGTAGTGATATTGACTATTATTACGGGGATTACTGTACTGGTTATTACCAGAAGGAGGA
GGACCGGAAAGTATGAGAAGGTCGAGATCAAGGAGATGGGTGAAATGAGACGAGGGCAGAACTCATAG

Alignment

ORF - retro_psin_22 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.3 %
• Parental protein coverage: 95.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAKIACSCATNKRTTNCSMSSGTCQCTSFGSQVLVNCQTLTSKCLLMKAEMAALKKSGRRERPKHAYVDN
          .A..AC.CATN.RT......SG.C.C.S.GS...V.C..LTSKCLLMKAEM....K..R...P.....DN
Retrocopy SAQKACTCATNRRTQCSEDISGNCLCRSVGSNQRVDCSVLTSKCLLMKAEMSP-SKARRFSKPELGFLDN

Parental  DGIYDPDCENSGKFKARQCNGT-SCWCVNTAGVRRTEKSDADLQCSELVRTSWILIETQHGERSKDVDVS
          DGIY.PDCE.SG.FKARQCN.T..CWCVNTAGVRRT.K.D..L.CSELVRT.WI..E..H.ERS......
Retrocopy DGIYNPDCEDSGIFKARQCNQTDTCWCVNTAGVRRTDKGDKNLRCSELVRTNWIFLELKHKERSEPFQAA

Parental  QLKETIKNEFRRRYLLEPKYIHDVVYEKPLIIIELKQNVSQKSSQDVDIADVAYYFEKDVKGDSLL-VTN
          ............RY.L.PKYI....YE.P.I.I.LKQN.SQKS..DVDIADVAYYFEKDVKGDS.....N
Retrocopy EVASGLRQIIQNRYKLHPKYITAIEYEYPFIHIDLKQNASQKSRGDVDIADVAYYFEKDVKGDSIFDPSN

Parental  PLVINVSEEPLKLDQTLIYYVDEKPPEFSMKRLTAGVIAVIVVVVLAIVAGIIVLVITRRRR-GKYEKTE
          .....VS..PL.....LIYYVDEKPPEFSMKRLTAGVIAV..VV.L.I..GI.VLVITRRRR.GKYEK.E
Retrocopy AFNLSVSGQPLDVEGILIYYVDEKPPEFSMKRLTAGVIAVLAVVILTIITGITVLVITRRRRTGKYEKVE

Parental  IKEMNEMQRELN
          IKEM.EM.R..N
Retrocopy IKEMGEMRRGQN

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_22 retrocopy.

TSS

Pelodiscus sinensis was not studied using FANTOM5 data.

Lab

retro_psin_22 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 17 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006474	1 retrocopy	retro_btau_66,
Choloepus hoffmanni	ENSCHOG00000013834	1 retrocopy	retro_chof_258,
Callithrix jacchus	ENSCJAG00000000624	1 retrocopy	retro_cjac_3006,
Dasypus novemcinctus	ENSDNOG00000011799	1 retrocopy	retro_dnov_345,
Erinaceus europaeus	ENSEEUG00000009462	1 retrocopy	retro_eeur_151,
Macropus eugenii	ENSMEUG00000015074	2 retrocopies	retro_meug_1984, retro_meug_474,
Microcebus murinus	ENSMICG00000000151	1 retrocopy	retro_mmur_739,
Macaca mulatta	ENSMMUG00000012390	1 retrocopy	retro_mmul_34,
Monodelphis domestica	ENSMODG00000001077	1 retrocopy	retro_mdom_104,
Mus musculus	ENSMUSG00000045394	1 retrocopy	retro_mmus_185,
Ochotona princeps	ENSOPRG00000004301	1 retrocopy	retro_opri_1225,
Pelodiscus sinensis	ENSPSIG00000015680	1 retrocopy	retro_psin_22 ,
Pan troglodytes	ENSPTRG00000011902	1 retrocopy	retro_ptro_92,
Rattus norvegicus	ENSRNOG00000015667	1 retrocopy	retro_rnor_252,
Sus scrofa	ENSSSCG00000008429	1 retrocopy	retro_sscr_69,
Ictidomys tridecemlineatus	ENSSTOG00000008631	1 retrocopy	retro_itri_106,
Tursiops truncatus	ENSTTRG00000004235	2 retrocopies	retro_ttru_21, retro_ttru_394,