RetrogeneDB ID: retro_sscr_891

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 6:137860503..137860848(-)
• Located in intron of: ENSSSCG00000003816

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJC19
• Ensembl ID: ENSSSCG00000011770
• Aliases: None
• Description: DnaJ (Hsp40) homolog, subfamily C, member 19 [Source:HGNC Symbol;Acc:30528]

Sequence

>retro_sscr_891
ATGGCCAGTACAGTGGTAGCAGCTGGACTGACCATTGCTGCCACAGGATTTGCAGGCCGTTATACTTTCCAAGCCATGAA
GCATATGGAGCCTCAAGTAAAACAAATTTTTCAAAGTCTACCAAAATCTGCCTTTCATGGTGGCTATTATAGAGTTGGGT
TTGAACCCAAAATGGTGACGTGGGAAGCAGCATTAATACTAGGTATAAGCCCTACTGCCAATAAAGGAAAAATAAGAGAT
GCTCACCAAAAAATTACGCTTTTAAATCACCCTGAGGGAGGATCTCCTTATACAGTGGCCAAAATCAATGAAGCTAAAGA
TTTACTAGAAGGTCAAGGTAAAAAA

Alignment

ORF - retro_sscr_891 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.62 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASTVVAVGLTIAAAGFAGRYALQAMKHMEPQVKQVFQSLPKSAFSGGYYRGGFEPKMTKREAALILGVS
          MASTVVA.GLTIAA.GFAGRY..QAMKHMEPQVKQ.FQSLPKSAF.GGYYR.GFEPKM...EAALILG.S
Retrocopy MASTVVAAGLTIAATGFAGRYTFQAMKHMEPQVKQIFQSLPKSAFHGGYYRVGFEPKMVTWEAALILGIS

Parental  PTANKGKIRDAHRRIMLLNHPDKGGSPYIAAKINEAKDLLEGQAKK
          PTANKGKIRDAH..I.LLNHP..GGSPY..AKINEAKDLLEGQ.KK
Retrocopy PTANKGKIRDAHQKITLLNHPE-GGSPYTVAKINEAKDLLEGQGKK

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP014902_placenta	0.00 RPM	7.17 RPM
SRP014902_testis	0.00 RPM	13.15 RPM
SRP018288_heart	0.00 RPM	62.05 RPM
SRP018288_kidney	0.00 RPM	68.26 RPM
SRP018288_liver	0.00 RPM	54.05 RPM
SRP018288_lung	0.00 RPM	14.56 RPM
SRP018856_adipose	0.00 RPM	23.90 RPM
SRP035408_brain	0.00 RPM	42.56 RPM
SRP035408_liver	0.00 RPM	56.25 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_891 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_891 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_891 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 103 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000023513	1 retrocopy	retro_btau_127,
Callithrix jacchus	ENSCJAG00000012795	10 retrocopies	retro_cjac_1008, retro_cjac_1192, retro_cjac_1364, retro_cjac_1430, retro_cjac_1550, retro_cjac_252, retro_cjac_2609, retro_cjac_2890, retro_cjac_3060, retro_cjac_914,
Cavia porcellus	ENSCPOG00000021198	1 retrocopy	retro_cpor_126,
Dasypus novemcinctus	ENSDNOG00000019067	1 retrocopy	retro_dnov_49,
Erinaceus europaeus	ENSEEUG00000006955	9 retrocopies	retro_eeur_221, retro_eeur_230, retro_eeur_309, retro_eeur_455, retro_eeur_48, retro_eeur_511, retro_eeur_596, retro_eeur_74, retro_eeur_94,
Echinops telfairi	ENSETEG00000006897	7 retrocopies	retro_etel_1071, retro_etel_1222, retro_etel_1559, retro_etel_275, retro_etel_384, retro_etel_81, retro_etel_821,
Ficedula albicollis	ENSFALG00000008296	1 retrocopy	retro_falb_28,
Gallus gallus	ENSGALG00000008852	1 retrocopy	retro_ggal_17,
Gorilla gorilla	ENSGGOG00000009120	7 retrocopies	retro_ggor_1037, retro_ggor_1483, retro_ggor_1484, retro_ggor_1783, retro_ggor_2365, retro_ggor_491, retro_ggor_517,
Loxodonta africana	ENSLAFG00000001910	5 retrocopies	retro_lafr_48, retro_lafr_515, retro_lafr_611, retro_lafr_881, retro_lafr_929,
Microcebus murinus	ENSMICG00000010381	4 retrocopies	retro_mmur_1160, retro_mmur_225, retro_mmur_320, retro_mmur_728,
Myotis lucifugus	ENSMLUG00000006865	1 retrocopy	retro_mluc_84,
Macaca mulatta	ENSMMUG00000012104	3 retrocopies	retro_mmul_2142, retro_mmul_2454, retro_mmul_946,
Otolemur garnettii	ENSOGAG00000008754	11 retrocopies	retro_ogar_1214, retro_ogar_1334, retro_ogar_138, retro_ogar_1625, retro_ogar_1811, retro_ogar_2012, retro_ogar_2048, retro_ogar_2881, retro_ogar_301, retro_ogar_442, retro_ogar_718,
Pongo abelii	ENSPPYG00000014328	2 retrocopies	retro_pabe_2126, retro_pabe_44,
Sus scrofa	ENSSSCG00000011770	2 retrocopies	retro_sscr_651, retro_sscr_891 ,
Tupaia belangeri	ENSTBEG00000015089	27 retrocopies	retro_tbel_1126, retro_tbel_1166, retro_tbel_1167, retro_tbel_1296, retro_tbel_1301, retro_tbel_1491, retro_tbel_1693, retro_tbel_1780, retro_tbel_2117, retro_tbel_2136, retro_tbel_2267, retro_tbel_2459, retro_tbel_266, retro_tbel_2830, retro_tbel_3233, retro_tbel_3303, retro_tbel_3556, retro_tbel_3716, retro_tbel_3814, retro_tbel_384, retro_tbel_3849, retro_tbel_3963, retro_tbel_4043, retro_tbel_42, retro_tbel_633, retro_tbel_833, retro_tbel_889,
Tarsius syrichta	ENSTSYG00000001611	3 retrocopies	retro_tsyr_112, retro_tsyr_174, retro_tsyr_312,
Tursiops truncatus	ENSTTRG00000014700	6 retrocopies	retro_ttru_1023, retro_ttru_1630, retro_ttru_1830, retro_ttru_662, retro_ttru_704, retro_ttru_962,
Vicugna pacos	ENSVPAG00000003387	1 retrocopy	retro_vpac_533,