RetrogeneDB ID: retro_hsap_873

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 11:49455027..49455990(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000226268
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SLC25A33
• Ensembl ID: ENSG00000171612
• Aliases: None
• Description: solute carrier family 25 (pyrimidine nucleotide carrier), member 33 [Source:HGNC Symbol;Acc:29681]

Sequence

>retro_hsap_873
ATGGCGACGGGCGGCCAGCAGAAGGAGAACACGCTGCTTCACCTCTTCGCCGGCGGGTGTGGAGGCACAGTTGGTGCTAT
TTTCACTTGTCCACTAGAAGTCATTAAGACACGGTTGCAGTCTTTAAGATTAGCTCTCCGGACAGTCTACTATCCTCAGG
TTCATCTGGGGACCATTAGTGGAGCTGGAATGGTGAGACCAACATCCGTGACACCTGGACTCTTTCAGGTTCTGAAGTCG
ATCTTGGAGAAAGAGGGACCAAAGTCACTTTTTAGAGGCTTGGGTCCAAATTTGGTTGGAGTTGCACCATCAAGGGCTGT
ATACTTTGCATGTTACTCCAAAGCCAAAGAGCAATTTAATGGCATTTTCGTGCCTAACAGCAATATTGTGCATATTTTCT
CAGCTGGCTCTGCAGCTTTTATCACAAATTCCTTAATGAATCCTATATGGATGGTTAAAACCCGAATGCAGCTAGAACAG
AAAGTGAGGGGCTTTAAGCAGGTGAATACACTCCAGTGTGCTCGTTACGTTTACCAGACCGAAGGCATTCGTGGCTTCTA
TAGAGGATTAACTGCCTCGTATGCTGGAATTTCCGAAACTATAATCTGCTTTGCTATTTATGAAAGTTTAAAGAAGTATC
TGAAAGAAGCTCCATTAGCCTCTTCTGCAAATGGGACTGAGAAAAATTCCACAAGTTTTTTTGGACTTATGGCAGCTGCT
GCTCTTTCTAAGGGCTGTGCCTCCTGCATTGCTTATCCACACGAAGTTATAAGGACGAGGCTCCGGGAAGAGGGCACCAA
GTACAAGTCTTTTGTCCAGACGGCGCGCCTGGTGTTCCAGGAAGAAGGCTACCTCGCCTTTTATAGAGGACTGTTTGCCC
AGCTTATCCGGCGGATCCCAAATACTGCCATTGTGTTGTCTACTTATGAGTTAATTGTGTACCTGTTAGAAGACCGTACT
CAG

Alignment

ORF - retro_hsap_873 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.44 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATGGQQKENTLLHLFAGGCGGTVGAIFTCPLEVIKTRLQSSRLALRTVYYPQVHLGTISGAGMVRPTSV
          MATGGQQKENTLLHLFAGGCGGTVGAIFTCPLEVIKTRLQS.RLALRTVYYPQVHLGTISGAGMVRPTSV
Retrocopy MATGGQQKENTLLHLFAGGCGGTVGAIFTCPLEVIKTRLQSLRLALRTVYYPQVHLGTISGAGMVRPTSV

Parental  TPGLFQVLKSILEKEGPKSLFRGLGPNLVGVAPSRAVYFACYSKAKEQFNGIFVPNSNIVHIFSAGSAAF
          TPGLFQVLKSILEKEGPKSLFRGLGPNLVGVAPSRAVYFACYSKAKEQFNGIFVPNSNIVHIFSAGSAAF
Retrocopy TPGLFQVLKSILEKEGPKSLFRGLGPNLVGVAPSRAVYFACYSKAKEQFNGIFVPNSNIVHIFSAGSAAF

Parental  ITNSLMNPIWMVKTRMQLEQKVRGSKQMNTLQCARYVYQTEGIRGFYRGLTASYAGISETIICFAIYESL
          ITNSLMNPIWMVKTRMQLEQKVRG.KQ.NTLQCARYVYQTEGIRGFYRGLTASYAGISETIICFAIYESL
Retrocopy ITNSLMNPIWMVKTRMQLEQKVRGFKQVNTLQCARYVYQTEGIRGFYRGLTASYAGISETIICFAIYESL

Parental  KKYLKEAPLASSANGTEKNSTSFFGLMAAAALSKGCASCIAYPHEVIRTRLREEGTKYKSFVQTARLVFR
          KKYLKEAPLASSANGTEKNSTSFFGLMAAAALSKGCASCIAYPHEVIRTRLREEGTKYKSFVQTARLVF.
Retrocopy KKYLKEAPLASSANGTEKNSTSFFGLMAAAALSKGCASCIAYPHEVIRTRLREEGTKYKSFVQTARLVFQ

Parental  EEGYLAFYRGLFAQLIRQIPNTAIVLSTYELIVYLLEDRTQ
          EEGYLAFYRGLFAQLIR.IPNTAIVLSTYELIVYLLEDRTQ
Retrocopy EEGYLAFYRGLFAQLIRRIPNTAIVLSTYELIVYLLEDRTQ

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
bodymap2_adipose	0.06 RPM	7.26 RPM
bodymap2_adrenal	0.43 RPM	5.26 RPM
bodymap2_brain	0.98 RPM	20.16 RPM
bodymap2_breast	0.51 RPM	35.21 RPM
bodymap2_colon	0.10 RPM	6.28 RPM
bodymap2_heart	0.00 RPM	11.32 RPM
bodymap2_kidney	0.68 RPM	21.45 RPM
bodymap2_liver	0.32 RPM	27.92 RPM
bodymap2_lung	0.05 RPM	4.15 RPM
bodymap2_lymph_node	0.02 RPM	5.19 RPM
bodymap2_ovary	0.19 RPM	7.33 RPM
bodymap2_prostate	0.38 RPM	8.16 RPM
bodymap2_skeletal_muscle	0.15 RPM	22.73 RPM
bodymap2_testis	11.44 RPM	27.51 RPM
bodymap2_thyroid	0.06 RPM	11.86 RPM
bodymap2_white_blood_cells	0.02 RPM	5.79 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_873 was not detected

EST

13 EST(s) were mapped to retro_hsap_873 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AA352224	49455579	49455766	100	187	0	187
AA398466	49454974	49455380	99.6	404	2	402
AA401872	49455019	49455393	99.8	372	1	370
AA757281	49454976	49455435	99.8	458	1	457
AA844723	49454973	49455385	100	412	0	412
AI200893	49454963	49455467	100	499	0	498
AI201028	49454967	49455426	99.8	458	1	457
AI201164	49454963	49455463	99	500	0	498
AW235374	49454976	49455337	97.8	360	1	356
BF059403	49454976	49455337	100	361	0	361
HY199799	49454979	49455441	99.8	460	1	458
HY212112	49454979	49455426	100	447	0	447
HY239480	49454979	49455409	100	430	0	430

TSS

No TSS is located nearby retro_hsap_873 retrocopy 5' end.

Lab

retro_hsap_873 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_873 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000424	1 retrocopy	retro_cjac_2186,
Dasypus novemcinctus	ENSDNOG00000014396	1 retrocopy	retro_dnov_2369,
Homo sapiens	ENSG00000171612	1 retrocopy	retro_hsap_873 ,
Gorilla gorilla	ENSGGOG00000006766	1 retrocopy	retro_ggor_709,
Monodelphis domestica	ENSMODG00000003059	1 retrocopy	retro_mdom_1512,
Otolemur garnettii	ENSOGAG00000007103	1 retrocopy	retro_ogar_2098,