RetrogeneDB ID: retro_psin_42

Retrocopy location

• Organism: Chinese softshell turtle (Pelodiscus sinensis)
• Coordinates: JH207674.1:296913..297519(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ST13
• Ensembl ID: ENSPSIG00000004553
• Aliases: None
• Description: suppression of tumorigenicity 13 (colon carcinoma) (Hsp70 interacting protein) [Source:HGNC Symbol;Acc:11343]

Sequence

>retro_psin_42
GAAAAGAAAACCAAGGAGGAAGGGTCACCAGAGGCAGCAGAGATCAAGGAGAGTGATTTGGAAATTGATGGTGATGTTGA
ACCAGATCTGGATGGTTCCCAAGAAATAGGAGATGAACATTTGGTAGTAACAAATGAATTGATAGACTCTGCCAACAGAA
AAAGGAAAGAGGCCTTTTCCTCTCTAGAGAAAGGTGACCTTCAGAAAGCTATGGATTTGTTCACAGATGCTATCAAGCTG
AATCCTCACTTCCACCTCTCATATGTTAATCGAGCCAGTGTCTTTTTGAAACTACAGAAGCCAAATGCTGCCATTAGAGA
CTGTGACAGAGCCTGTGAGCTTAACCCCAATTCAGCACAGTCTTACAAGTGGAGAGGGCAAGCACACATGCTCCTGGGAT
GCTGGGAAAAGGCAGCTCAGGACTTGACCTTGGCATGTCAACTGGATTATGATGAAAACACTTATACCAGGCTAAAAAAG
GTGCTAATGGCTGAGAAGATTGCTGCACATCAGGCAGAGTATGAGCAAAAATGTGCATTAAGGGAGATACAGGAAAGGCT
GGAAAGGGTGAAACTGGCCTTGGAGGAGGAAGAAAGAATCCAGAGG

Alignment

ORF - retro_psin_42 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.54 %
• Parental protein coverage: 63.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EKQPEEPVKSPEPESEESDLEIDNEGVIEPDKDDPQEMGDENVEVTEEMMDQADEKKIEGIHALGEGELQ
          EK...E.......E..ESDLEID..G..EPD.D..QE.GDE...VT.E..D.A..K..E....L..G.LQ
Retrocopy EKKTKEEGSPEAAEIKESDLEID--GDVEPDLDGSQEIGDEHLVVTNELIDSANRKRKEAFSSLEKGDLQ

Parental  KAIDLFTEAIKLNPHLAILYAKRASVFVKLQKPNAAIRDCDRAIQINPDSAQTYKWRGKAHRLLGHWEEA
          KA.DLFT.AIKLNPH....Y..RASVF.KLQKPNAAIRDCDRA...NP.SAQ.YKWRG.AH.LLG.WE.A
Retrocopy KAMDLFTDAIKLNPHFHLSYVNRASVFLKLQKPNAAIRDCDRACELNPNSAQSYKWRGQAHMLLGCWEKA

Parental  VHDLALACKLDYDEEASAMLKEVQPRAQKIVEHRRKYERKREEKEIKERLERVKKAREEHERAQR
          ..DL.LAC.LDYDE.....LK.V...A.KI..H...YE.K....EI.ERLERVK.A.EE.ER.QR
Retrocopy AQDLTLACQLDYDENTYTRLKKVL-MAEKIAAHQAEYEQKCALREIQERLERVKLALEEEERIQR

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_42 retrocopy.

TSS

Pelodiscus sinensis was not studied using FANTOM5 data.

Lab

retro_psin_42 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 16 parental genes, and 79 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000005227	1 retrocopy	retro_acar_2,
Ailuropoda melanoleuca	ENSAMEG00000013880	1 retrocopy	retro_amel_135,
Bos taurus	ENSBTAG00000006202	4 retrocopies	retro_btau_254, retro_btau_427, retro_btau_621, retro_btau_658,
Canis familiaris	ENSCAFG00000001139	14 retrocopies	retro_cfam_1029, retro_cfam_1101, retro_cfam_1122, retro_cfam_1239, retro_cfam_1467, retro_cfam_1830, retro_cfam_1950, retro_cfam_1958, retro_cfam_247, retro_cfam_262, retro_cfam_582, retro_cfam_808, retro_cfam_901, retro_cfam_969,
Callithrix jacchus	ENSCJAG00000004644	11 retrocopies	retro_cjac_1843, retro_cjac_1953, retro_cjac_2177, retro_cjac_2275, retro_cjac_2789, retro_cjac_3123, retro_cjac_3570, retro_cjac_4019, retro_cjac_488, retro_cjac_640, retro_cjac_685,
Cavia porcellus	ENSCPOG00000002290	4 retrocopies	retro_cpor_1394, retro_cpor_1477, retro_cpor_166, retro_cpor_961,
Felis catus	ENSFCAG00000011847	2 retrocopies	retro_fcat_920, retro_fcat_987,
Gorilla gorilla	ENSGGOG00000026747	16 retrocopies	retro_ggor_1600, retro_ggor_1734, retro_ggor_1791, retro_ggor_1975, retro_ggor_2177, retro_ggor_2634, retro_ggor_2692, retro_ggor_277, retro_ggor_3045, retro_ggor_629, retro_ggor_666, retro_ggor_749, retro_ggor_788, retro_ggor_832, retro_ggor_833, retro_ggor_938,
Myotis lucifugus	ENSMLUG00000007764	2 retrocopies	retro_mluc_1088, retro_mluc_2021,
Macaca mulatta	ENSMMUG00000019118	3 retrocopies	retro_mmul_1842, retro_mmul_402, retro_mmul_438,
Monodelphis domestica	ENSMODG00000013042	2 retrocopies	retro_mdom_1087, retro_mdom_31,
Otolemur garnettii	ENSOGAG00000016932	1 retrocopy	retro_ogar_224,
Pongo abelii	ENSPPYG00000011858	14 retrocopies	retro_pabe_1004, retro_pabe_2181, retro_pabe_2361, retro_pabe_2657, retro_pabe_2885, retro_pabe_3183, retro_pabe_3673, retro_pabe_3794, retro_pabe_437, retro_pabe_554, retro_pabe_727, retro_pabe_763, retro_pabe_798, retro_pabe_880,
Pelodiscus sinensis	ENSPSIG00000004553	1 retrocopy	retro_psin_42 ,
Sarcophilus harrisii	ENSSHAG00000000319	2 retrocopies	retro_shar_70, retro_shar_767,
Ictidomys tridecemlineatus	ENSSTOG00000003165	1 retrocopy	retro_itri_88,